Error in names(stats) in aucprTestAlongTree

[MichaelPeibo]

Hi, I follow the code in supplementary analysis, as below:

# Determine tips to run DE for
tips.to.run <- setdiff(as.character(object@tree$segment.names), c("Primoridal Germ Cells", "EVL/Periderm"))
genes.use <- NULL # Calculate for all genes

# Calculate the markers of each other population.
gene.markers <- list()
for (tipn in 1:length(tips.to.run)) {
  tip <- tips.to.run[tipn]
  print(paste0(Sys.time(), ": ", tip))
  markers <- aucprTestAlongTree(object, pseudotime="pseudotime", tips=tip, log.effect.size=0.4, auc.factor = 1.25, max.auc.threshold = 0.85, frac.must.express = 0.1, frac.min.diff = 0, genes.use=genes.use, root="7", only.return.global=F, must.beat.sibs=0.6, report.debug=T, segs.to.skip = NULL)
  saveRDS(markers, file=paste0("cascades/aucpr/", tip, ".rds"))
  gene.markers[[tip]] <- markers
}

However, I got the error, Unknown is one of my tip:

[1] "2019-06-02 21:17:16: Unknown"
Error in names(stats) <- c("n.1", "n.2", "pt.1.mean", "pt.2.mean", "pt.1.median",  :
  'names' attribute [14] must be the same length as the vector [10]
In addition: Warning messages:
1: In if (format == "unary") { :
  the condition has length > 1 and only the first element will be used
2: In mean.default(object@meta[cells.1, "n.Genes"]) :
  argument is not numeric or logical: returning NA
3: In mean.default(object@meta[cells.2, "n.Genes"]) :
  argument is not numeric or logical: returning NA
4: In mean.default(object@meta[cells.1, "n.Trans"]) :
  argument is not numeric or logical: returning NA
5: In mean.default(object@meta[cells.2, "n.Trans"]) :
  argument is not numeric or logical: returning NA

Any suggestion how do I get this error? Thanks!

[MichaelPeibo]

My object info is this, my guess is somewhere is not matching.

str(urd.tree) Formal class 'URD' [package "URD"] with 22 slots ..@ count.data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. ..@ i : int [1:26415129] 12 14 27 32 39 40 42 52 57 85 ... .. .. ..@ p : int [1:10953] 0 2277 4893 6832 9105 11460 14357 17330 20097 22160 ... .. .. ..@ Dim : int [1:2] 20660 10952 .. .. ..@ Dimnames:List of 2 .. .. .. ..$ : chr [1:20660] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ... .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. ..@ x : num [1:26415129] 1 1 1 1 1 1 1 1 1 1 ... .. .. ..@ factors : list() ..@ logupx.data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. ..@ i : int [1:26415129] 12 14 27 32 39 40 42 52 57 85 ... .. .. ..@ p : int [1:10953] 0 2277 4893 6832 9105 11460 14357 17330 20097 22160 ... .. .. ..@ Dim : int [1:2] 20660 10952 .. .. ..@ Dimnames:List of 2 .. .. .. ..$ : chr [1:20660] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ... .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. ..@ x : num [1:26415129] 1.68 1.68 1.68 1.68 1.68 ... .. .. ..@ factors : list() ..@ meta :'data.frame': 10952 obs. of 10 variables: .. ..$ orig.ident : chr [1:10952] "day21" "day21" "day21" "day21" ... .. ..$ percent.mito : num [1:10952] 0.0428 0.0379 0.0475 0.0416 0.0253 ... .. ..$ S.Score : num [1:10952] 0.3912 0.4648 -0.1564 -0.0511 0.5198 ... .. ..$ G2M.Score : num [1:10952] 0.188 0.234 -0.345 -0.151 -0.23 ... .. ..$ Phase : Factor w/ 3 levels "G1","G2M","S": 3 3 1 1 3 3 2 3 3 3 ... .. ..$ CC.Difference: num [1:10952] 0.203 0.231 0.189 0.1 0.75 ... .. ..$ percent.rp : num [1:10952] 0.364 0.297 0.275 0.296 0.319 ... .. ..$ nCount_RNA : num [1:10952] 6899 8359 4779 6440 6769 ... .. ..$ nFeature_RNA : int [1:10952] 2277 2616 1939 2273 2355 2897 2973 2767 2063 2735 ... .. ..$ stage : chr [1:10952] "day21" "day21" "day21" "day21" ... ..@ group.ids :'data.frame': 10952 obs. of 13 variables: .. ..$ orig.ident : chr [1:10952] "day21" "day21" "day21" "day21" ... .. ..$ Phase : Factor w/ 3 levels "G1","G2M","S": 3 3 1 1 3 3 2 3 3 3 ... .. ..$ stage : chr [1:10952] "day21" "day21" "day21" "day21" ... .. ..$ RNA_snn_res.0.6 : Factor w/ 9 levels "0","1","2","3",..: 1 1 1 1 1 1 1 1 1 1 ... .. ..$ seurat_clusters : Factor w/ 12 levels "0","1","2","3",..: 1 1 1 1 1 1 1 1 1 1 ... .. ..$ RNA_snn_res.0.5 : Factor w/ 6 levels "0","1","2","3",..: 1 2 2 1 2 1 1 2 2 2 ... .. ..$ RNA_snn_res.0.3 : Factor w/ 5 levels "0","1","2","3",..: 1 2 2 1 1 1 1 2 2 2 ... .. ..$ RNA_snn_res.0.55: Factor w/ 7 levels "0","1","2","3",..: 1 2 2 1 2 2 2 2 2 2 ... .. ..$ RNA_snn_res.0.58: Factor w/ 8 levels "0","1","2","3",..: 3 1 1 1 1 1 1 1 1 1 ... .. ..$ RNA_snn_res.1 : Factor w/ 12 levels "0","1","2","3",..: 1 1 1 1 1 1 1 1 1 1 ... .. ..$ tip.clusters : Factor w/ 2 levels "5","6": NA NA NA NA NA NA NA NA NA NA ... .. ..$ segment : chr [1:10952] "7" "7" "7" "7" ... .. ..$ node : chr [1:10952] "7-1" "7-41" "7-45" "7-1" ... ..@ var.genes : chr [1:2000] "STMN2" "DDIT4" "HIST1H4C" "IGFBP5" ... ..@ knn : list() ..@ pca.sdev : num [1:50] 5.57 4.43 3.5 2.97 2.7 ... ..@ pca.load :'data.frame': 1161 obs. of 50 variables: .. ..$ PC_1 : num [1:1161] -0.110127 0.002374 -0.015139 -0.000681 -0.013308 ... .. ..$ PC_2 : num [1:1161] -0.013441 0.159761 0.039274 0.000709 -0.001807 ... .. ..$ PC_3 : num [1:1161] -0.00942 -0.01552 0.05726 -0.01306 -0.02325 ... .. ..$ PC_4 : num [1:1161] -0.05082 0.01531 0.11387 0.00211 -0.0041 ... .. ..$ PC_5 : num [1:1161] -0.004519 -0.013273 -0.081612 -0.000737 0.001874 ... .. ..$ PC_6 : num [1:1161] 0.000129 0.001217 -0.142956 0.010713 -0.016587 ... .. ..$ PC_7 : num [1:1161] 0.00631 -0.04868 -0.03505 -0.06287 0.01329 ... .. ..$ PC_8 : num [1:1161] 0.0054 -0.07256 0.07666 -0.04841 0.00227 ... .. ..$ PC_9 : num [1:1161] 0.01086 0.02047 -0.01032 0.00615 -0.01855 ... .. ..$ PC_10: num [1:1161] -0.004126 0.0393 -0.005008 0.055743 -0.000476 ... .. ..$ PC_11: num [1:1161] -0.0051 0.0471 -0.0389 0.0106 -0.0038 ... .. ..$ PC_12: num [1:1161] 0.01217 -0.0113 -0.00742 0.02547 0.01445 ... .. ..$ PC_13: num [1:1161] -0.00534 -0.00569 -0.01644 -0.05779 -0.02081 ... .. ..$ PC_14: num [1:1161] -0.00515 0.00791 0.00686 0.11538 -0.02201 ... .. ..$ PC_15: num [1:1161] -0.0016 -0.00638 -0.02996 0.06744 0.02242 ... .. ..$ PC_16: num [1:1161] -0.00778 -0.00671 -0.0394 0.04462 -0.0346 ... .. ..$ PC_17: num [1:1161] 0.000445 0.022045 -0.042571 -0.015983 -0.004472 ... .. ..$ PC_18: num [1:1161] 0.00204 0.04505 -0.04934 -0.04388 -0.00617 ... .. ..$ PC_19: num [1:1161] -0.0074 -0.02536 0.00618 -0.02088 -0.00851 ... .. ..$ PC_20: num [1:1161] 0.00118 0.03223 -0.05815 -0.01732 0.00268 ... .. ..$ PC_21: num [1:1161] 0.00441 -0.02284 -0.05153 0.01849 0.01103 ... .. ..$ PC_22: num [1:1161] 0.00751 -0.01476 -0.05303 0.06439 -0.00544 ... .. ..$ PC_23: num [1:1161] -0.00501 -0.01699 -0.02053 -0.00876 0.0061 ... .. ..$ PC_24: num [1:1161] -0.01996 -0.01952 0.00027 0.06576 0.00323 ... .. ..$ PC_25: num [1:1161] -0.00278 0.00327 -0.01267 0.01892 -0.02527 ... .. ..$ PC_26: num [1:1161] -0.0052 -0.00055 0.04939 0.02805 -0.00194 ... .. ..$ PC_27: num [1:1161] 0.000684 -0.01559 0.004375 0.00021 -0.007003 ... .. ..$ PC_28: num [1:1161] -0.00497 -0.01765 0.00825 -0.01865 0.01537 ... .. ..$ PC_29: num [1:1161] -0.00611 -0.01003 -0.01808 -0.04536 -0.00869 ... .. ..$ PC_30: num [1:1161] 0.00269 -0.01391 -0.00663 -0.00965 -0.0208 ... .. ..$ PC_31: num [1:1161] 0.00346 -0.0137 0.00131 -0.02322 -0.00179 ... .. ..$ PC_32: num [1:1161] -0.000612 0.041159 0.063658 -0.01291 -0.010784 ... .. ..$ PC_33: num [1:1161] 0.00725 0.01816 -0.05645 -0.02712 -0.01926 ... .. ..$ PC_34: num [1:1161] -0.01518 0.01555 -0.0036 -0.00536 -0.0258 ... .. ..$ PC_35: num [1:1161] 0.00897 -0.02634 0.02983 0.00881 0.00169 ... .. ..$ PC_36: num [1:1161] 0.0207 0.0132 -0.01 0.0217 -0.0205 ... .. ..$ PC_37: num [1:1161] 0.01308 0.01273 0.0052 -0.01276 -0.00314 ... .. ..$ PC_38: num [1:1161] 0.012579 0.000329 0.008517 -0.02146 -0.014338 ... .. ..$ PC_39: num [1:1161] 0.00555 0.02237 0.02376 0.02357 0.0002 ... .. ..$ PC_40: num [1:1161] 0.00742 0.01749 -0.01316 -0.01367 0.02682 ... .. ..$ PC_41: num [1:1161] -0.00234 0.00919 -0.03656 0.00262 -0.00417 ... .. ..$ PC_42: num [1:1161] -0.01242 0.01347 -0.04788 0.03004 -0.00192 ... .. ..$ PC_43: num [1:1161] 0.000536 -0.012699 0.007828 -0.015072 -0.000177 ... .. ..$ PC_44: num [1:1161] -0.01039 -0.00433 -0.00374 -0.0039 0.00246 ... .. ..$ PC_45: num [1:1161] 0.001946 -0.027575 -0.014983 -0.019516 -0.000506 ... .. ..$ PC_46: num [1:1161] 0.00861 -0.01033 0.0144 0.01514 0.00126 ... .. ..$ PC_47: num [1:1161] 0.00109 0.03715 -0.02585 -0.00261 0.00879 ... .. ..$ PC_48: num [1:1161] -0.00871 0.01003 0.01612 -0.03094 -0.00753 ... .. ..$ PC_49: num [1:1161] 0.01807 0.00588 -0.01466 0.01543 0.00686 ... .. ..$ PC_50: num [1:1161] 0.00842 0.01451 -0.02575 0.00387 0.00762 ... ..@ pca.scores :'data.frame': 10952 obs. of 50 variables: .. ..$ PC_1 : num [1:10952] 4.05 3.15 3.56 4.22 5.34 ... .. ..$ PC_2 : num [1:10952] -0.791 -1.061 -1.982 -2.847 0.565 ... .. ..$ PC_3 : num [1:10952] -0.418 0.395 3.748 -0.465 -0.659 ... .. ..$ PC_4 : num [1:10952] -2.207 -0.74 -1.418 -0.826 -0.18 ... .. ..$ PC_5 : num [1:10952] 2.79 1.48 1.32 2.79 3.8 ... .. ..$ PC_6 : num [1:10952] 5.37 1.19 -2.22 2.26 1.15 ... .. ..$ PC_7 : num [1:10952] -2.7644 -1.1468 1.6591 -0.0712 -1.4275 ... .. ..$ PC_8 : num [1:10952] -0.291 1.8766 -0.7868 0.059 -0.0801 ... .. ..$ PC_9 : num [1:10952] 0.574 2.709 -1.352 -0.852 2.518 ... .. ..$ PC_10: num [1:10952] 1.038 1.462 -0.104 -1.314 0.761 ... .. ..$ PC_11: num [1:10952] -3.349 -0.366 1.417 1.191 -1.827 ... .. ..$ PC_12: num [1:10952] 2.424 1.962 2.016 -0.388 -0.726 ... .. ..$ PC_13: num [1:10952] -0.571 0.783 -0.581 -1.544 -0.788 ... .. ..$ PC_14: num [1:10952] 1.144 0.705 -2.61 0.17 2.247 ... .. ..$ PC_15: num [1:10952] -0.972 -0.914 0.405 -0.954 0.49 ... .. ..$ PC_16: num [1:10952] -0.8377 0.0974 0.7453 -0.1886 0.5486 ... .. ..$ PC_17: num [1:10952] 0.669 0.277 -0.163 -0.17 -0.342 ... .. ..$ PC_18: num [1:10952] 0.147 -1.505 0.386 -1.595 -2.133 ... .. ..$ PC_19: num [1:10952] -0.529 -0.748 -0.704 0.488 0.286 ... .. ..$ PC_20: num [1:10952] -1.06 1.16 1.03 -1.73 -1.7 ... .. ..$ PC_21: num [1:10952] 1.0885 0.0681 0.7799 0.7128 1.3149 ... .. ..$ PC_22: num [1:10952] 1.3525 -0.2064 -0.0337 -1.2915 1.0358 ... .. ..$ PC_23: num [1:10952] 0.227 0.815 0.476 1.016 2.747 ... .. ..$ PC_24: num [1:10952] -0.725 0.378 0.484 -0.382 -1.478 ... .. ..$ PC_25: num [1:10952] -1.0289 -0.033 -0.438 -0.0032 -1.3752 ... .. ..$ PC_26: num [1:10952] 0.187 -0.552 1.513 0.205 -0.405 ... .. ..$ PC_27: num [1:10952] -0.353 -0.476 -0.637 -0.208 -0.87 ... .. ..$ PC_28: num [1:10952] -0.0122 1.6606 -1.1728 -0.9998 0.4002 ... .. ..$ PC_29: num [1:10952] -0.897 0.832 1.396 0.797 1.014 ... .. ..$ PC_30: num [1:10952] -0.797 -0.351 -1.864 -2.168 0.687 ... .. ..$ PC_31: num [1:10952] 0.394 0.649 -0.791 1.285 -2.084 ... .. ..$ PC_32: num [1:10952] -2.4539 -0.2073 0.0821 0.8248 1.0019 ... .. ..$ PC_33: num [1:10952] -0.482 -1.265 -0.806 0.27 -0.499 ... .. ..$ PC_34: num [1:10952] -1.906 1.825 -0.796 -0.234 0.438 ... .. ..$ PC_35: num [1:10952] 1.4941 -0.7323 0.0537 -0.3784 -1.504 ... .. ..$ PC_36: num [1:10952] -0.283 -1.64 1.16 1.996 0.377 ... .. ..$ PC_37: num [1:10952] 1.752 -0.197 -1.213 -0.858 1.889 ... .. ..$ PC_38: num [1:10952] -1.067 -2.053 1.759 0.965 -0.588 ... .. ..$ PC_39: num [1:10952] -2.356 0.727 0.417 -1.696 -1.111 ... .. ..$ PC_40: num [1:10952] 0.88 -0.243 -0.035 -1.19 0.291 ... .. ..$ PC_41: num [1:10952] -0.387 0.206 -2.123 -0.805 -0.087 ... .. ..$ PC_42: num [1:10952] 0.291 1.1091 -1.7466 -0.4103 -0.0745 ... .. ..$ PC_43: num [1:10952] -0.394 -0.774 1.462 -0.358 -0.27 ... .. ..$ PC_44: num [1:10952] -0.662 0.41 2.193 -0.091 2.036 ... .. ..$ PC_45: num [1:10952] -1.1093 0.0113 0.1328 -0.2737 -0.0465 ... .. ..$ PC_46: num [1:10952] 1.204 0.833 -0.538 0.785 1.089 ... .. ..$ PC_47: num [1:10952] 1.007 -0.763 -2.024 0.229 -0.532 ... .. ..$ PC_48: num [1:10952] -0.479 -1.126 0.769 0.264 -0.544 ... .. ..$ PC_49: num [1:10952] -0.7084 0.1724 0.637 -0.1606 0.0641 ... .. ..$ PC_50: num [1:10952] -1.51 0.489 2.477 0.446 0.726 ... ..@ pca.sig : logi [1:50] TRUE TRUE FALSE FALSE FALSE FALSE ... ..@ tsne.y :'data.frame': 10952 obs. of 2 variables: .. ..$ tSNE1: num [1:10952] 0.49 0.403 -1.096 0.169 1.115 ... .. ..$ tSNE2: num [1:10952] 1.125 -0.495 -0.523 0.331 0.147 ... ..@ plot.3d : list() ..@ gene.sig.z :'data.frame': 0 obs. of 0 variables Formal class 'data.frame' [package "methods"] with 4 slots .. .. ..@ .Data : list() .. .. ..@ names : chr(0) .. .. ..@ row.names: int(0) .. .. ..@ .S3Class : chr "data.frame" ..@ dm :Formal class 'DiffusionMap' [package "destiny"] with 17 slots .. .. ..@ eigenvalues : num [1:200] 0.966 0.937 0.859 0.819 0.779 ... .. .. ..@ eigenvectors : num [1:10952, 1:200] -0.00575 -0.00608 -0.00132 -0.00336 -0.00479 ... .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. .. .. ..$ : chr [1:200] "DC1" "DC2" "DC3" "DC4" ... .. .. ..@ sigmas :Formal class 'Sigmas' [package "destiny"] with 5 slots .. .. .. .. ..@ log_sigmas : NULL .. .. .. .. ..@ dim_norms : NULL .. .. .. .. ..@ optimal_sigma: num 16 .. .. .. .. ..@ optimal_idx : NULL .. .. .. .. ..@ avrd_norms : NULL .. .. ..@ data_env :<environment: 0x953b41e0a8> .. .. ..@ eigenvec0 : num [1:10952] -0.00565 -0.0058 -0.00669 -0.00607 -0.00653 ... .. .. ..@ transitions :Formal class 'dsCMatrix' [package "Matrix"] with 7 slots .. .. .. .. ..@ i : int [1:2040379] 3 6 2 5 12 4 5 9 10 17 ... .. .. .. .. ..@ p : int [1:10953] 0 0 0 0 0 0 1 1 1 1 ... .. .. .. .. ..@ Dim : int [1:2] 10952 10952 .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. .. .. ..@ x : num [1:2040379] 0.01931 0.01731 0.00349 0.00302 0.00295 ... .. .. .. .. ..@ uplo : chr "U" .. .. .. .. ..@ factors : list() .. .. ..@ d : num [1:10952] 27.7 32.6 26.7 33.5 29 ... .. .. ..@ d_norm : num [1:10952] 0.00461 0.00486 0.00647 0.00532 0.00615 ... .. .. ..@ k : num 200 .. .. ..@ n_local : num [1:3] 5 6 7 .. .. ..@ density_norm : logi TRUE .. .. ..@ rotate : logi FALSE .. .. ..@ distance : chr "euclidean" .. .. ..@ censor_val : NULL .. .. ..@ censor_range : NULL .. .. ..@ missing_range: NULL .. .. ..@ vars : NULL ..@ diff.data :'data.frame': 10779 obs. of 10 variables: .. ..$ visitfreq.raw.pseudotime: num [1:10779] 100 100 100 99 100 100 100 100 100 100 ... .. ..$ visitfreq.log.pseudotime: num [1:10779] 2 2 2 2 2 ... .. ..$ visitfreq.raw.5 : num [1:10779] 62 4 255 9 86 8 111 22 26 7 ... .. ..$ visitfreq.log.5 : num [1:10779] 1.799 0.699 2.408 1 1.94 ... .. ..$ visitfreq.raw.6 : num [1:10779] 10 2 102 5 53 0 49 14 5 7 ... .. ..$ visitfreq.log.6 : num [1:10779] 1.041 0.477 2.013 0.778 1.732 ... .. ..$ visitfreq.raw.7 : num [1:10779] 44.33 3.32 203.01 7.64 74.79 ... .. ..$ visitfreq.log.7 : num [1:10779] 1.656 0.636 2.31 0.937 1.88 ... .. ..$ segment : chr [1:10779] "5" "5" "5" "5" ... .. ..$ node : chr [1:10779] "5-8" "5-6" "5-2" "5-5" ... ..@ pseudotime :'data.frame': 10952 obs. of 3 variables: .. ..$ pseudotime: num [1:10952] 0 0.142 0.168 0 0.142 ... .. ..$ 5 : num [1:10952] 1 NA 0.845 1 0.828 ... .. ..$ 6 : num [1:10952] 1 0.863 0.869 1 0.836 ... ..@ pseudotime.stability:List of 2 .. ..$ pseudotime : num [1:10952, 1:10] NA NA NA 1 NA ... .. .. ..- attr(, "dimnames")=List of 2 .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. .. ..$ : chr [1:10] "25000" "50000" "75000" "1e+05" ... .. ..$ walks.per.cell: num [1:10952, 1:10] NA NA NA 1 NA NA 2 NA 3 NA ... .. .. ..- attr(, "dimnames")=List of 2 .. .. .. ..$ : chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. .. .. ..$ : chr [1:10] "25000" "50000" "75000" "1e+05" ... ..@ tree :List of 22 .. ..$ cells.in.tip :List of 2 .. .. ..$ 5: chr [1:1090] "mda_day28_CTGAAACAGGGATCTG" "mda_day28_GGATTACTCCTTTCTC" "mda_day21_AAACCTGTCCGGGTGT" "mda_day21_AAACGGGAGATACACA" ... .. .. ..$ 6: chr [1:561] "mda_day21_CCAATCCCAGGGCATA" "mda_day35_ATAAGAGGTACGAAAT" "mda_day35_GAGCAGACACTCTGTC" "mda_day35_TACCTTAGTTGGACCC" ... .. ..$ tips : chr [1:2] "5" "6" .. ..$ pseudotime : Named num [1:10952] 0 0.142 0.168 0 0.142 ... .. .. ..- attr(, "names")= chr [1:10952] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. ..$ segment.pseudotime.limits :'data.frame': 3 obs. of 2 variables: .. .. ..$ start: num [1:3] 0.265 0.265 0 .. .. ..$ end : num [1:3] 0.445 0.547 0.265 .. ..$ segment.divergence :'data.frame': 1 obs. of 3 variables: .. .. ..$ seg.1 : chr "5" .. .. ..$ seg.2 : chr "6" .. .. ..$ pseudotime.breakpoint: num 0.265 .. ..$ pseudotime.breakpoint.details:List of 1 .. .. ..$ 5-6:List of 4 .. .. .. ..$ cells.considered: int 9578 .. .. .. ..$ breakpoint : num 0.265 .. .. .. ..$ cells.in.windows:List of 108 .. .. .. .. ..$ : chr [1:400] "mda_day21_CAGCTGGAGAGTACCG" "mda_day21_GCGCAGTTCACGCGGT" "mda_day21_TACGGGCAGATAGCAT" "mda_day21_TTGAACGGTATCGCAT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_ACGGCCACAGTAAGAT" "mda_day21_ACGGCCATCTACTTAC" "mda_day21_ACGGGCTCAGGCTCAC" "mda_day21_ACGGGTCCACCCTATC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_ATCACGACACCCAGTG" "mda_day21_ATCACGAGTTAAGATG" "mda_day21_ATCATCTAGGAGTACC" "mda_day21_ATCATGGTCCGGCACA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CAGCGACTCCCTCTTT" "mda_day21_CAGCGACTCCTTGACC" "mda_day21_CAGCGACTCGGCGCTA" "mda_day21_CAGCTGGAGGCTAGCA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CCTACCAAGGGAGTAA" "mda_day21_CCTACCACAAAGAATC" "mda_day21_CCTACCACACCGAAAG" "mda_day21_CCTACCATCGACGGAA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CGTGTCTCAATTCCTT" "mda_day21_CGTTAGAGTGATGATA" "mda_day21_CGTTCTGAGAAGGACA" "mda_day21_CGTTGGGTCATCTGTT" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GACGGCTCATGCAACT" "mda_day21_GACGTGCAGAAGGTTT" "mda_day21_GACGTGCAGAGACTAT" "mda_day21_GACGTGCCATCCAACA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GGAACTTGTTGGTAAA" "mda_day21_GGAACTTTCCAAAGTC" "mda_day21_GGAATAAAGTGCCAGA" "mda_day21_GGACAAGTCAACGAAA" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_GTCTTCGGTGCAACTT" "mda_day21_GTCTTCGTCTTACCTA" "mda_day21_GTGAAGGTCCTTGGTC" "mda_day21_GTGCGGTCATCCGGGT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TCAGATGGTAAGTGGC" "mda_day21_TCAGCTCCACCATGTA" "mda_day21_TCAGGTACAAAGGCGT" "mda_day21_TCAGGTACAAGTTAAG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGGCGCAGTTGGTAAA" "mda_day21_TGGCTGGAGTGGGCTA" "mda_day21_TGGCTGGGTAGCAAAT" "mda_day21_TGGCTGGGTCGCGGTT" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CCTCAGTCACACTGCG" "mda_day28_CGATGTACACATGACT" "mda_day28_CGCGTTTAGGAGTCTG" "mda_day28_CGTCCATCATGGAATA" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_GATGAAAAGGGAGTAA" "mda_day21_GCTGCAGGTGTGAAAT" "mda_day21_GGATTACTCCAAGTAC" "mda_day21_GGCCGATAGGGAGTAA" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TCTCATATCTGTGCAA" "mda_day21_TGACTAGGTTGCGCAC" "mda_day21_TGCGTGGTCCTGTAGA" "mda_day21_TGGTTAGCATCGGACC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_AAGGTTCAGTACGCCC" "mda_day21_AAGTCTGAGAGACGAA" "mda_day21_AAGTCTGAGCCCAATT" "mda_day21_AATCCAGTCTACTCAT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_AGCTCTCGTAGCAAAT" "mda_day21_AGGCCACCAACTTGAC" "mda_day21_AGGCCACTCGAGAGCA" "mda_day21_AGGCCGTAGTGGCACA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CAGCAGCCAAGTCTGT" "mda_day21_CAGCATAAGTGTCTCA" "mda_day21_CAGCATACATGATCCA" "mda_day21_CAGCATAGTTCCACAA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CGACCTTTCAGCTCTC" "mda_day21_CGACTTCGTCTTCTCG" "mda_day21_CGAGCACGTCTTGTCC" "mda_day21_CGAGCCACAATCTGCA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CTCTACGAGTTTAGGA" "mda_day21_CTCTACGCACGTGAGA" "mda_day21_CTCTGGTAGAATGTTG" "mda_day21_CTCTGGTGTACTCGCG" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GCAATCATCCGTTGTC" "mda_day21_GCACATACACGCCAGT" "mda_day21_GCACATAGTCTAGTCA" "mda_day21_GCACTCTGTCGAACAG" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GTAGGCCCAACTGCGC" "mda_day21_GTAGGCCCAGGACGTA" "mda_day21_GTAGTCATCCTTTACA" "mda_day21_GTAGTCATCTGGTATG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TACTTACTCCTGTAGA" "mda_day21_TACTTGTGTCGCGGTT" "mda_day21_TAGACCAGTAAGGGCT" "mda_day21_TAGACCATCCAATGGT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGCTGCTCAGCTATTG" "mda_day21_TGCTGCTGTTACGACT" "mda_day21_TGCTGCTTCCCAAGAT" "mda_day21_TGGACGCCATATACGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_AACGTTGAGATATGCA" "mda_day28_ACGAGGATCCGTCAAA" "mda_day28_AGAATAGCAAACTGCT" "mda_day28_AGAGCTTCAGCCAGAA" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_TGAGAGGTCGACAGCC" "mda_day28_TTGCCGTGTAGTGAAT" "mda_day35_AACGTTGAGTCACGCC" "mda_day35_CACAGTATCACCAGGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_ACGTCAACAACGATGG" "mda_day21_ACTATCTAGCGCCTTG" "mda_day21_ACTATCTAGTTAGCGG" "mda_day21_ACTGATGCACTAAGTC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_GCAGCCAGTGCCTGCA" "mda_day21_GCAGTTAGTAGAAAGG" "mda_day21_GCGCAACAGACTACAA" "mda_day21_GCGCAGTGTCCGTCAG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CGAACATAGAGCTTCT" "mda_day21_CGAATGTCAGTCGATT" "mda_day21_CGAATGTGTTCGCTAA" "mda_day21_GCGCAACTCCACGAAT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_ACGGGCTTCCCACTTG" "mda_day21_ACGGGTCAGTTCGATC" "mda_day21_ACGTCAAAGATACACA" "mda_day21_ACTATCTTCTCTAAGG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CAGCATAAGCTCCCAG" "mda_day21_CAGCCGACATGCAATC" "mda_day21_CAGCGACCACGGTAAG" "mda_day21_CAGCGACCAGTCACTA" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CTCACACTCTGTACGA" "mda_day21_CTCATTAAGACAAAGG" "mda_day21_CTCATTACACCATCCT" "mda_day21_CTCCTAGGTCAGAATA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GCGCAGTCACCCATTC" "mda_day21_GCGCCAAGTTTAGCTG" "mda_day21_GCGCCAATCACTTACT" "mda_day21_GCGCGATGTTTGGGCC" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GTTCTCGTCAACCATG" "mda_day21_GTTTCTACACCGAATT" "mda_day21_TACCTATCAAGAGGCT" "mda_day21_TACCTATCAAGGTTTC" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_TTAGTTCAGAAACGAG" "mda_day21_TTATGCTAGCAGGCTA" "mda_day21_TTATGCTCAAGCCGTC" "mda_day21_TTATGCTCATTGAGCT" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_TCTCTAATCTCCGGTT" "mda_day28_TGACTTTTCGAGAGCA" "mda_day28_TGCACCTGTACACCGC" "mda_day28_TGCGTGGCACAGACTT" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_TGGTTAGGTTCCACGG" "mda_day28_TGTATTCTCACGGTTA" "mda_day28_TTAGGCAAGCAGACTG" "mda_day28_TTCCCAGGTTAAGGGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CATCGGGAGTAATCCC" "mda_day21_CATGGCGCAGCTGTTA" "mda_day21_CCAATCCTCGAACTGT" "mda_day21_CCACGGATCCTAGGGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TTAGGACCAGATAATG" "mda_day21_TTAGGCAAGTGGTAAT" "mda_day21_TTATGCTAGAGTCTGG" "mda_day21_TTCTACAGTGCGGTAA" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CGGACTGGTCAAAGAT" "mda_day28_CGTGTCTAGCGCCTCA" "mda_day28_CTAAGACCAAGCGAGT" "mda_day28_CTCTACGGTGACGGTA" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGCGTGGTCATGCAAC" "mda_day21_TGCTGCTAGCCGTCGT" "mda_day21_TGCTGCTGTGGTAACG" "mda_day21_TTGACTTAGCGGCTTC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CCTTTCTTCTGACCTC" "mda_day28_CGGACGTGTCTCTTTA" "mda_day21_AGACGTTTCGCAAACT" "mda_day21_ATCATCTTCAGCCTAA" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CGACCTTGTCTCCACT" "mda_day28_CTAGAGTAGTTGTCGT" "mda_day35_TAGCCGGTCCAGAGGA" "mda_day35_TACCTTAGTTGGACCC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_TGCTACCGTAGCGCAA" "mda_day28_TTTACTGCAATTCCTT" "mda_day21_ACACCAAGTGATAAGT" "mda_day28_GTCTTCGAGACTAGGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CGGACACTCGCAAACT" "mda_day21_TACCTTAGTCTCACCT" "mda_day28_GACGCGTCAGGGTACA" "mda_day28_ATCATGGGTTCTGAAC" ... .. .. .. .. ..$ : chr [1:401] "mda_day35_ACGGGCTAGGACTGGT" "mda_day28_ACTGTCCCACATGACT" "mda_day28_ACTTGTTTCTGTACGA" "mda_day21_CATGGCGGTGACGCCT" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GGACAAGTCCATGAAC" "mda_day35_GCATACATCTGATACG" "mda_day28_GGCCGATAGAGCCTAG" "mda_day21_GGGCACTAGTAGTGCG" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_AGATTGCCAAGTCTAC" "mda_day35_ACACTGACACGTCTCT" "mda_day28_GCATGATTCAGTTCGA" "mda_day21_CGTGTCTTCTCTGCTG" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_TTAGGCAAGTTTGCGT" "mda_day21_CCTCTGAAGCAATATG" "mda_day28_AGGGTGATCATCTGCC" "mda_day21_ACCAGTACAAAGTCAA" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_AGCATACTCACCATAG" "mda_day21_CTCTACGTCCTGCCAT" "mda_day21_GTTCATTAGCACACAG" "mda_day35_TACTTGTAGAAGAAGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GCGAGAACACATTTCT" "mda_day28_TCTGGAAGTTTGGGCC" "mda_day28_AACCATGTCTCCAACC" "mda_day21_CACTCCATCACTGGGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CATCAGAAGAAACCGC" "mda_day28_CGAGCCATCGAGAACG" "mda_day21_AGGCCGTCATATGGTC" "mda_day35_CCCAATCTCCTGTACC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TCCCGATTCGCAGGCT" "mda_day28_CCTACCACATTAACCG" "mda_day35_CCTAAAGTCGTCTGAA" "mda_day28_AAGGTTCCACGGTGTC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_GTGCGGTCAAGCTGAG" "mda_day21_GACGCGTAGACAGGCT" "mda_day35_TTCTCAAGTAAAGTCA" "mda_day35_TTTGCGCGTACCGAGA" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_ACCAGTAGTCGCGGTT" "mda_day28_CCGTGGAAGTCCGGTC" "mda_day35_CGCGTTTAGCGATTCT" "mda_day35_CATCGGGGTAAATGTG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGGCCAGTCGGTCTAA" "mda_day35_TTTGTCATCATGGTCA" "mda_day35_CTGCCTATCCAAACAC" "mda_day21_ACGATGTCAGGCAGTA" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_ACACTGAGTGCCTGGT" "mda_day21_TAAGCGTAGGGTGTGT" "mda_day35_CGAACATTCAAGATCC" "mda_day28_CCAGCGAGTCCTCCAT" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_GACGCGTGTTCCACAA" "mda_day28_GTGTTAGGTTAGAACA" "mda_day35_TCTGAGACACTGTCGG" "mda_day28_CAGCTAAAGTACACCT" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CTCACACGTCTAAAGA" "mda_day35_CTACACCAGAGTGAGA" "mda_day21_CGTAGGCGTCGAATCT" "mda_day28_CAGCGACCATACGCCG" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GTTCATTAGCCAGTTT" "mda_day35_CTAAGACGTAAGAGGA" "mda_day28_CGATGGCTCTCTTGAT" "mda_day21_TACGGGCCAGACAGGT" ... .. .. .. .. ..$ : chr [1:401] "mda_day35_TGTATTCGTTACGTCA" "mda_day21_AGTCTTTTCTTGAGGT" "mda_day35_GGATGTTTCTTTAGGG" "mda_day21_GGATTACCATGGTAGG" ... .. .. .. .. ..$ : chr [1:401] "mda_day35_AGACGTTTCATGCATG" "mda_day35_GGTGCGTCAAGTAATG" "mda_day28_TTAGTTCGTGATGTCT" "mda_day28_GCATGATTCAACACTG" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_GGTGTTATCATCGATG" "mda_day21_CATCGGGGTACGACCC" "mda_day28_CCCTCCTGTACAGTGG" "mda_day35_GTGCGGTAGATACACA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CGCCAAGAGAGCTATA" "mda_day28_CAGTAACGTTCCACAA" "mda_day21_GTCATTTAGACTTGAA" "mda_day28_TCTATTGTCATGGTCA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_ACTGCTCTCTTCAACT" "mda_day28_GATGAGGCAATGACCT" "mda_day21_CTAATGGTCAGAGACG" "mda_day28_CTACGTCGTCGCGTGT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGGGAAGCACCGAATT" "mda_day35_AATCCAGAGCATGGCA" "mda_day28_TCAGATGGTCCAACTA" "mda_day35_GGCTCGAAGGCTAGAC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_GGCGACTAGTACGCGA" "mda_day35_CTCGTACGTTACCAGT" "mda_day35_CGAGCACCACAGAGGT" "mda_day21_ACTTACTGTATAGTAG" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_CATCGGGGTACCGTAT" "mda_day35_CTCACACTCCTCGCAT" "mda_day28_CGACCTTAGGACATTA" "mda_day35_ATTATCCTCGACAGCC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_GCATACACAGTCTTCC" "mda_day35_GCTTGAAGTACCGTTA" "mda_day35_TGTTCCGAGAGAGCTC" "mda_day35_AGAGCTTCATCTCGCT" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_CTAACTTTCACGACTA" "mda_day35_GCTTGAACATGGTTGT" "mda_day28_CGCGTTTAGGTAGCTG" "mda_day28_TCTCATATCGGATGTT" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_CGATCGGCACGCGAAA" "mda_day21_CCGGTAGAGACAGGCT" "mda_day21_GGCGTGTTCTGCTGTC" "mda_day28_CGGGTCAAGCGATATA" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_GAAATGAAGACCACGA" "mda_day28_CCGGGATAGTGGCACA" "mda_day35_GGTGCGTAGCGACGTA" "mda_day21_ATTGGACGTCAAAGCG" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GGGACCTGTTCCACGG" "mda_day35_ACTTTCAAGGAGTCTG" "mda_day21_GTATTCTGTCTAGTGT" "mda_day28_CAGCTAATCGCACTCT" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_TTGAACGGTCAAACTC" "mda_day35_TGGGAAGAGATGGGTC" "mda_day35_GACACGCGTTTCGCTC" "mda_day35_GCGACCAGTCGTGGCT" ... .. .. .. .. ..$ : chr [1:401] "mda_day35_TACGGTAAGGTGTGGT" "mda_day35_GCGAGAATCCATGAAC" "mda_day28_ACTTTCATCCTTTACA" "mda_day28_CGTTCTGTCTGGTTCC" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GCGCAGTTCTGCGGCA" "mda_day35_ACTTTCAAGCGTGAAC" "mda_day35_TAAGCGTTCCACTGGG" "mda_day21_ATGCGATTCCTGTACC" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_AACCATGGTAAGGGCT" "mda_day35_CTGTGCTAGGCATGTG" "mda_day35_AGCAGCCCACATCTTT" "mda_day21_GATGAAAGTAGCACGA" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_ATTCTACCATTCCTCG" "mda_day28_TACGGATGTCAACATC" "mda_day35_CTAATGGCAAAGGCGT" "mda_day21_GCTGCGAAGATCGGGT" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_AGGGAGTAGTGGCACA" "mda_day35_TAGTGGTGTGCACGAA" "mda_day21_GACGGCTTCTTGTATC" "mda_day28_GTGCGGTTCAGAGCTT" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CGTCCATGTCTAAACC" "mda_day28_TTGACTTCAGCTGTGC" "mda_day35_CATTCGCGTCAACATC" "mda_day28_TAGACCAAGACCTTTG" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_ATGGGAGGTTAGAACA" "mda_day35_GCGCAGTAGTGTTAGA" "mda_day35_GACTGCGAGGAACTGC" "mda_day35_ATCGAGTTCCAAATGC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CGGACTGTCAGCACAT" "mda_day35_GAACCTACACGGTGTC" "mda_day21_TACTCGCGTCCAAGTT" "mda_day21_CTCATTAGTGGAAAGA" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_TCTATTGCATGCCCGA" "mda_day28_AGTGAGGGTACTTGAC" "mda_day28_ATTGGACAGTGTGAAT" "mda_day35_GCAGCCAAGTACACCT" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CAACCTCGTCAGGACA" "mda_day35_TTGACTTGTAGCTAAA" "mda_day21_AATCGGTCAGGTCCAC" "mda_day21_CAGTAACTCACGAAGG" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TGACTAGAGAAGGACA" "mda_day35_GTCGGGTTCTTCATGT" "mda_day21_TAGTTGGGTCCCTTGT" "mda_day21_CTTTGCGTCCAAGTAC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_TTCGGTCGTCTGATCA" "mda_day35_ATCCACCCAATACGCT" "mda_day35_TCTCATAGTCTGATTG" "mda_day35_GTCTCGTTCAAACGGG" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GTTACAGGTAGCTAAA" "mda_day21_AAGGAGCTCATTGCGA" "mda_day35_TGCACCTTCAGTTCGA" "mda_day28_GCTGCTTCATCCCATC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_TAAACCGAGTATCGAA" "mda_day28_TTGCGTCGTGCTTCTC" "mda_day35_TCTCATAAGCCACGCT" "mda_day21_TGAGGGAAGCTAGTTC" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CCTAAAGTCCGCAGTG" "mda_day21_ATTATCCCAACACGCC" "mda_day35_GTGCAGCTCATTGCCC" "mda_day28_ACACCAAAGTCGTACT" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_CACAGTAAGATGTAAC" "mda_day28_TGAGCCGTCTCGGACG" "mda_day35_GGAAAGCCAATTCCTT" "mda_day28_TCCCGATCAGGAATGC" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_GACCAATTCAAACCAC" "mda_day28_CATTCGCCAAGTTGTC" "mda_day35_TGGTTCCTCTACTATC" "mda_day21_CTTTGCGGTCAGATAA" ... .. .. .. .. ..$ : chr [1:401] "mda_day28_ACTGATGAGTTATCGC" "mda_day35_CGTGTAAGTATATGGA" "mda_day28_TTCCCAGCACTTCGAA" "mda_day28_TCTGGAATCAGGATCT" ... .. .. .. .. ..$ : chr [1:401] "mda_day21_ACATACGCACGGACAA" "mda_day28_CAGCTGGGTAGGACAC" "mda_day35_GCTGCGAAGAGACGAA" "mda_day28_CATTCGCGTAAGTTCC" ... .. .. .. .. ..$ : chr [1:400] "mda_day21_CAACTAGAGTTCGCAT" "mda_day35_CATTCGCTCCTTGGTC" "mda_day35_GACGTTACACTGTCGG" "mda_day35_GTATCTTCAAGTCATC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_ACCCACTCATGTAGTC" "mda_day21_CTGCGGATCACTCCTG" "mda_day28_ACTTACTAGATGGCGT" "mda_day28_CAAGAAATCATCATTC" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GAGCAGAGTAAAGTCA" "mda_day28_CGATCGGGTTGGTAAA" "mda_day35_TGACGGCTCTTGTTTG" "mda_day28_TCAGATGGTAGGGTAC" ... .. .. .. .. ..$ : chr [1:400] "mda_day35_TGCCCATGTGCCTGTG" "mda_day35_ACTTACTCACAAGTAA" "mda_day28_AGCTCTCCATGGTAGG" "mda_day21_TGACTAGGTGTCCTCT" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CCTCTGATCGGATGGA" "mda_day35_CCGTACTAGTCAAGGC" "mda_day35_GAGGTGACACCAGTTA" "mda_day28_CTAATGGTCCTTTCGG" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_CTAAGACAGTCAATAG" "mda_day21_GAACGGACAAGACGTG" "mda_day28_TTGTAGGTCGAATGGG" "mda_day28_TCAGATGCATGCATGT" ... .. .. .. .. ..$ : chr [1:400] "mda_day28_GTTCATTTCTCATTCA" "mda_day35_ACACCGGAGAGACTTA" "mda_day28_CAGAGAGCAGGATCGA" "mda_day35_CGTGTAAGTAAGTGGC" ... .. .. .. .. .. [list output truncated] .. .. .. ..$ details :'data.frame': 108 obs. of 7 variables: .. .. .. .. ..$ p : num [1:108] 3.26e-08 2.10e-08 1.96e-07 2.28e-06 3.32e-06 ... .. .. .. .. ..$ mean.pseudotime : num [1:108] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. ..$ min.pseudotime : num [1:108] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. ..$ max.pseudotime : num [1:108] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. ..$ cells.visited.seg1: num [1:108] 400 400 400 401 401 401 401 401 400 400 ... .. .. .. .. ..$ cells.visited.seg2: num [1:108] 165 168 166 172 191 192 192 192 160 136 ... .. .. .. .. ..$ different : logi [1:108] TRUE TRUE TRUE TRUE TRUE TRUE ... .. ..$ segment.joins :'data.frame': 2 obs. of 3 variables: .. .. ..$ parent : chr [1:2] "7" "7" .. .. ..$ child : chr [1:2] "5" "6" .. .. ..$ pseudotime: num [1:2] 0.265 0.265 .. ..$ segments : chr [1:3] "5" "6" "7" .. ..$ segment.joins.initial :'data.frame': 2 obs. of 3 variables: .. .. ..$ parent : chr [1:2] "7" "7" .. .. ..$ child : chr [1:2] "5" "6" .. .. ..$ pseudotime: num [1:2] 0.265 0.265 .. ..$ cells.in.segment :List of 3 .. .. ..$ 5: chr [1:1748] "mda_day28_AACACGTAGAAGGCCT" "mda_day28_AACCGCGGTTTGGCGC" "mda_day28_AGATCTGTCAACGCTA" "mda_day28_AGCGTATAGACAAAGG" ... .. .. ..$ 6: chr [1:1930] "mda_day28_AAACCTGAGTCCGTAT" "mda_day28_ACACTGACACATAACC" "mda_day28_ACCTTTAGTCAACTGT" "mda_day28_ACGGGCTGTGCAGGTA" ... .. .. ..$ 7: chr [1:7101] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ACAGCTATCTGCAGTA" "mda_day21_ATAAGAGAGACGACGT" "mda_day21_ATAAGAGGTAGGCTGA" ... .. ..$ cells.in.nodes :List of 107 .. .. ..$ 5-1 : chr [1:103] "mda_day28_TAAGTGCTCGTCTGAA" "mda_day21_GTTCTCGAGAAGGCCT" "mda_day21_TCAATCTTCCAAACAC" "mda_day21_ATCACGATCAGAAATG" ... .. .. ..$ 5-2 : chr [1:103] "mda_day21_AGCTTGAAGGCAAAGA" "mda_day28_AAACGGGCAACTGGCC" "mda_day28_TACTTACAGTGCGTGA" "mda_day28_TTCTCCTCATCACGAT" ... .. .. ..$ 5-3 : chr [1:102] "mda_day21_AATCGGTCAGGTCCAC" "mda_day21_CAGTAACTCACGAAGG" "mda_day35_TCGCGTTGTGGCTCCA" "mda_day28_CATGACAAGTGTCTCA" ... .. .. ..$ 5-4 : chr [1:103] "mda_day21_ATGGGAGTCACCCGAG" "mda_day35_CAGAATCCAATGTTGC" "mda_day35_AAGACCTCAAGTCTGT" "mda_day28_TTCTCCTGTGAGTATA" ... .. .. ..$ 5-5 : chr [1:103] "mda_day28_AGCGGTCCAAGTCTAC" "mda_day21_ATAACGCGTAGTACCT" "mda_day28_CATGGCGAGTCGTTTG" "mda_day21_CTCAGAACATTACCTT" ... .. .. ..$ 5-6 : chr [1:103] "mda_day21_TCAGGATGTTCCGTCT" "mda_day35_GGCCGATCACGGTAAG" "mda_day28_AACCGCGGTTTGGCGC" "mda_day21_CCCTCCTAGTAGTGCG" ... .. .. ..$ 5-7 : chr [1:103] "mda_day28_GTGCGGTCACAGGCCT" "mda_day35_ACCGTAATCGGCGGTT" "mda_day28_TCAGGTAGTAAGGGAA" "mda_day28_GGGTCTGCAGTAACGG" ... .. .. ..$ 5-8 : chr [1:103] "mda_day35_ACATCAGAGTCGCCGT" "mda_day28_GGGCATCTCTGACCTC" "mda_day28_AGAATAGTCCTCATTA" "mda_day28_ATCATCTTCAAGAAGT" ... .. .. ..$ 5-9 : chr [1:102] "mda_day35_CCTAGCTCATACGCCG" "mda_day21_TGACTTTTCAGTTCGA" "mda_day28_GTCGGGTCAGCTATTG" "mda_day28_ATTATCCTCCCTTGTG" ... .. .. ..$ 5-10: chr [1:103] "mda_day28_GGCGTGTAGAGTTGGC" "mda_day28_GGACAAGAGGTCATCT" "mda_day21_GTCTTCGCATAAAGGT" "mda_day28_GGATGTTCATGTCCTC" ... .. .. ..$ 5-11: chr [1:103] "mda_day28_TGTTCCGTCTCCAACC" "mda_day28_GTTACAGAGATGCCAG" "mda_day21_GAATGAATCAAGGTAA" "mda_day21_ACGGGCTCACGAAACG" ... .. .. ..$ 5-12: chr [1:103] "mda_day28_CTTGGCTTCACCCGAG" "mda_day28_CCTACCAAGTACATGA" "mda_day35_GGACGTCCATAAAGGT" "mda_day35_GGGACCTGTTCTGTTT" ... .. .. ..$ 5-13: chr [1:103] "mda_day35_CGTCTACGTTATGCGT" "mda_day28_GTTACAGCAGTTTACG" "mda_day28_GCGGGTTAGGCGATAC" "mda_day28_GGAGCAAAGTCTCAAC" ... .. .. ..$ 5-14: chr [1:103] "mda_day35_CATCGGGCACTGTTAG" "mda_day28_CAGCAGCAGTACTTGC" "mda_day28_TTCTACACAACAACCT" "mda_day28_CGCTGGATCGCCAGCA" ... .. .. ..$ 5-15: chr [1:102] "mda_day28_GTGCAGCTCGTCACGG" "mda_day28_ATCATGGCATGGTTGT" "mda_day28_AACCGCGGTAGAGGAA" "mda_day35_CTAGCCTGTAGCGTCC" ... .. .. ..$ 5-16: chr [1:103] "mda_day21_CGCTGGACATGTTCCC" "mda_day28_GATGAGGCACAACGCC" "mda_day35_GCACATACACCAGGTC" "mda_day28_CTCGGGAAGTGGAGTC" ... .. .. ..$ 5-17: chr [1:103] "mda_day28_CTCATTACAAACGCGA" "mda_day28_GCCTCTATCGGATGGA" "mda_day28_GGGAGATCATGCCTTC" "mda_day28_CGCTTCAGTGATAAAC" ... .. .. ..$ 6-1 : chr [1:102] "mda_day35_CCTCAGTCATTCTTAC" "mda_day35_CGTGAGCTCACGGTTA" "mda_day28_ATAAGAGGTGGGTCAA" "mda_day35_AGGGAGTAGTGGCACA" ... .. .. ..$ 6-2 : chr [1:101] "mda_day35_GAGGTGATCGTGTAGT" "mda_day35_TATCAGGTCTGGCGTG" "mda_day35_GAATGAATCCTAGTGA" "mda_day35_AACGTTGGTAGGCATG" ... .. .. ..$ 6-3 : chr [1:102] "mda_day35_TCTTCGGTCAGGTTCA" "mda_day35_AGCTTGAAGGGTATCG" "mda_day28_TGGACGCCAGGTCTCG" "mda_day28_CTAGAGTGTGAAATCA" ... .. .. ..$ 6-4 : chr [1:101] "mda_day35_TGGGAAGGTTATGTGC" "mda_day28_GATGCTATCCGTCATC" "mda_day35_TACTTGTTCCACGACG" "mda_day35_GGAACTTTCACGAAGG" ... .. .. ..$ 6-5 : chr [1:102] "mda_day35_ATGGGAGCAATTCCTT" "mda_day35_TGCACCTTCAGTTCGA" "mda_day28_CTGATAGAGTGGGCTA" "mda_day35_CGTAGCGCAACAACCT" ... .. .. ..$ 6-6 : chr [1:101] "mda_day35_GACTACACACTACAGT" "mda_day35_TCATTACTCGCATGAT" "mda_day35_GCAGTTATCATGTCCC" "mda_day35_AGGGATGAGGTCGGAT" ... .. .. ..$ 6-7 : chr [1:102] "mda_day35_GGTGTTATCACCTTAT" "mda_day28_CTGCGGACAATCGGTT" "mda_day35_CGACCTTAGCCAGTAG" "mda_day35_AGCGTCGTCACCTCGT" ... .. .. ..$ 6-8 : chr [1:102] "mda_day35_GATGCTACATTCCTGC" "mda_day28_CGTGTCTCAGATTGCT" "mda_day35_AGAGCGAGTATAAACG" "mda_day28_TACACGAAGAGAGCTC" ... .. .. ..$ 6-9 : chr [1:101] "mda_day35_GGAGCAATCAATCACG" "mda_day35_GAGGTGACACCAGTTA" "mda_day35_GACTACAAGTCATGCT" "mda_day35_CTGGTCTAGGACAGAA" ... .. .. ..$ 6-10: chr [1:102] "mda_day28_GCACATATCCGCTGTT" "mda_day28_GATCGTACAAGCCGCT" "mda_day28_CGCTGGATCAAGGTAA" "mda_day35_GATCGATTCCGCGTTT" ... .. .. ..$ 6-11: chr [1:101] "mda_day28_CATATTCTCGAGAGCA" "mda_day35_TGCGGGTGTTGTCGCG" "mda_day28_GTGCTTCAGGACAGAA" "mda_day28_CTGATAGTCCGAAGAG" ... .. .. ..$ 6-12: chr [1:102] "mda_day28_CTACGTCAGTCCAGGA" "mda_day35_CTCCTAGAGTGTACCT" "mda_day35_GGCGACTTCGGTGTCG" "mda_day28_TGTATTCGTTCCGGCA" ... .. .. ..$ 6-13: chr [1:102] "mda_day35_TCGCGAGGTGATGTGG" "mda_day35_CCAATCCGTACCGGCT" "mda_day35_GATGAAAGTCACCTAA" "mda_day35_GTTCGGGTCAATCTCT" ... .. .. ..$ 6-14: chr [1:101] "mda_day35_CGTTGGGGTTCCCTTG" "mda_day28_AGGCCGTCAGGAACGT" "mda_day35_GTAACTGTCGACCAGC" "mda_day35_TACGGTACAGCAGTTT" ... .. .. ..$ 6-15: chr [1:102] "mda_day35_AGCTCCTAGTATCTCG" "mda_day28_CGAGAAGAGTAATCCC" "mda_day35_CCTCAGTAGGCGACAT" "mda_day35_CTCGGAGGTAAAGGAG" ... .. .. ..$ 6-16: chr [1:101] "mda_day35_ATCATCTGTAGCTGCC" "mda_day35_CATATGGAGACTAGGC" "mda_day35_GCGACCATCTCGCATC" "mda_day35_TAGCCGGCATTTGCTT" ... .. .. ..$ 6-17: chr [1:102] "mda_day35_CAGCAGCAGCTGTCTA" "mda_day35_TAGAGCTGTAGAGTGC" "mda_day35_CGGGTCATCATCACCC" "mda_day35_GACGTGCGTCAGATAA" ... .. .. ..$ 6-18: chr [1:101] "mda_day35_GTAGTCAAGGTGCTAG" "mda_day28_GGGATGAGTAGTACCT" "mda_day35_GGTGCGTTCCCATTAT" "mda_day35_ACGGGTCCATGCAACT" ... .. .. ..$ 6-19: chr [1:102] "mda_day35_GGGATGACACTTAAGC" "mda_day35_TTGCGTCTCCATGCTC" "mda_day35_CTCGAAAAGAAGGTTT" "mda_day35_GTACGTAGTTGCTCCT" ... .. .. ..$ 7-1 : chr [1:100] "mda_day21_AATCGGTCAAGTCTGT" "mda_day21_ATAAGAGGTAGGCTGA" "mda_day21_CAGCTGGAGAGTACCG" "mda_day21_CCACTACCACATCCAA" ... .. .. ..$ 7-2 : chr [1:100] "mda_day21_ACACCAATCACAGTAC" "mda_day21_ACACCCTAGATGGGTC" "mda_day21_ACACCCTCAGCCACCA" "mda_day21_ACACCCTGTAGCCTCG" ... .. .. ..$ 7-3 : chr [1:100] "mda_day21_ACTTTCAGTTGAGTTC" "mda_day21_AGAATAGAGAATGTGT" "mda_day21_AGAATAGAGAGGTAGA" "mda_day21_AGAATAGAGTCTCAAC" ... .. .. ..$ 7-4 : chr [1:100] "mda_day21_AGTTGGTAGCGATTCT" "mda_day21_AGTTGGTCAAAGTCAA" "mda_day21_AGTTGGTCACGCATCG" "mda_day21_AGTTGGTGTACCGTAT" ... .. .. ..$ 7-5 : chr [1:100] "mda_day21_CAAGGCCCAATCGAAA" "mda_day21_CAAGGCCCAGCTCCGA" "mda_day21_CAAGGCCCATACGCTA" "mda_day21_CAAGGCCGTCATGCAT" ... .. .. ..$ 7-6 : chr [1:100] "mda_day21_CATATTCTCTACTCAT" "mda_day21_CATATTCTCTCGATGA" "mda_day21_CATCAAGAGGAGCGTT" "mda_day21_CATCAAGCATTAACCG" ... .. .. ..$ 7-7 : chr [1:100] "mda_day21_CCTACCACACCGAAAG" "mda_day21_CCTACCATCGACGGAA" "mda_day21_CCTAGCTAGATCTGCT" "mda_day21_CCTAGCTAGTCTCGGC" ... .. .. ..$ 7-8 : chr [1:100] "mda_day21_CGGAGTCTCTGCTTGC" "mda_day21_CGGCTAGCAGTCCTTC" "mda_day21_CGGCTAGCATCCGTGG" "mda_day21_CGGCTAGGTCTCGTTC" ... .. .. ..$ 7-9 : chr [1:100] "mda_day21_CTCGGGATCAGCAACT" "mda_day21_CTCGGGATCCATTCTA" "mda_day21_CTCGTACCAAGAAGAG" "mda_day21_CTCGTACTCGAGCCCA" ... .. .. ..$ 7-10: chr [1:100] "mda_day21_GACCAATGTAAGGATT" "mda_day21_GACCAATGTTGGTGGA" "mda_day21_GACCAATTCACTCCTG" "mda_day21_GACCTGGAGAGTCGGT" ... .. .. ..$ 7-11: chr [1:100] "mda_day21_GCATGATAGTCTCCTC" "mda_day21_GCATGATGTGAAATCA" "mda_day21_GCATGCGAGGTTCCTA" "mda_day21_GCATGCGCACATAACC" ... .. .. ..$ 7-12: chr [1:100] "mda_day21_GGCCGATTCTCCAGGG" "mda_day21_GGCGACTGTATGGTTC" "mda_day21_GGCGACTGTGGTTTCA" "mda_day21_GGCGACTTCAAAGTAG" ... .. .. ..$ 7-13: chr [1:100] "mda_day21_GTCATTTGTACAGTTC" "mda_day21_GTCATTTGTGAGTATA" "mda_day21_GTCATTTGTTCCCTTG" "mda_day21_GTCCTCAAGCTCCCAG" ... .. .. ..$ 7-14: chr [1:100] "mda_day21_TACGGATCATCTCCCA" "mda_day21_TACGGATTCGCTAGCG" "mda_day21_TACGGATTCTGCTGCT" "mda_day21_TACGGATTCTTGGGTA" ... .. .. ..$ 7-15: chr [1:100] "mda_day21_TCGGGACCACTATCTT" "mda_day21_TCGGGACGTATCAGTC" "mda_day21_TCGGGACGTGTGGTTT" "mda_day21_TCGGTAAAGAAACCTA" ... .. .. ..$ 7-16: chr [1:100] "mda_day21_TGGACGCTCGACGGAA" "mda_day21_TGGACGCTCTGTCTAT" "mda_day21_TGGCCAGTCAGAAATG" "mda_day21_TGGCCAGTCATATCGG" ... .. .. ..$ 7-17: chr [1:100] "mda_day21_TTGCGTCTCGAGAGCA" "mda_day21_TTGGAACCAAGCGTAG" "mda_day21_TTGGAACCATAGAAAC" "mda_day21_TTGGAACGTAGAGCTG" ... .. .. ..$ 7-18: chr [1:100] "mda_day28_GGCTGGTGTAGAGCTG" "mda_day28_GGGCACTAGGATATAC" "mda_day28_GTACGTATCAGGCCCA" "mda_day28_GTAGGCCGTTCAACCA" ... .. .. ..$ 7-19: chr [1:100] "mda_day28_CTCTACGAGGATGGAA" "mda_day28_CTGTGCTGTTCTGTTT" "mda_day28_CTGTTTAAGCTTATCG" "mda_day28_CTGTTTAGTCAGCTAT" ... .. .. ..$ 7-20: chr [1:100] "mda_day21_GGATTACTCCAAGTAC" "mda_day21_GGCCGATAGGGAGTAA" "mda_day21_GGGAATGGTGTGCCTG" "mda_day21_GGGCATCTCTTTCCTC" ... .. .. ..$ 7-21: chr [1:100] "mda_day21_ACTGAACGTTGGACCC" "mda_day21_ACTGTCCGTTTCGCTC" "mda_day21_AGAGCGAGTGCTTCTC" "mda_day21_AGGCCGTGTCTTGCGG" ... .. .. ..$ 7-22: chr [1:100] "mda_day21_ACATACGCAACTGGCC" "mda_day21_ACATACGCATGCCACG" "mda_day21_ACATACGGTCCTCTTG" "mda_day21_ACATACGTCGGCGCAT" ... .. .. ..$ 7-23: chr [1:100] "mda_day21_AGCGTCGGTCTAGCGC" "mda_day21_AGCGTCGTCTTCGGTC" "mda_day21_AGCTCTCAGATCTGCT" "mda_day21_AGCTCTCGTAGCAAAT" ... .. .. ..$ 7-24: chr [1:100] "mda_day21_CACACCTGTCTCGTTC" "mda_day21_CACACCTTCGCCCTTA" "mda_day21_CACACTCTCCGTCAAA" "mda_day21_CACAGGCTCAACGGGA" ... .. .. ..$ 7-25: chr [1:100] "mda_day21_CCCAATCAGGCTCTTA" "mda_day21_CCCAATCCACGACGAA" "mda_day21_CCCAATCGTAGCGTCC" "mda_day21_CCCAATCTCAGTTCGA" ... .. .. ..$ 7-26: chr [1:100] "mda_day21_CGGACTGTCATCTGCC" "mda_day21_CGGAGCTAGACTAGGC" "mda_day21_CGGAGCTAGGCATGTG" "mda_day21_CGGAGCTTCATTCACT" ... .. .. ..$ 7-27: chr [1:100] "mda_day21_CTGGTCTCATCCCACT" "mda_day21_CTGGTCTGTACTCAAC" "mda_day21_CTGGTCTGTATATGAG" "mda_day21_CTGTTTAAGATGTCGG" ... .. .. ..$ 7-28: chr [1:100] "mda_day21_GATGAGGGTCCTAGCG" "mda_day21_GATGAGGTCGCTTGTC" "mda_day21_GATGCTAAGCTTTGGT" "mda_day21_GATGCTAAGGATGTAT" ... .. .. ..$ 7-29: chr [1:100] "mda_day21_GGCGTGTCAGGAATCG" "mda_day21_GGCGTGTGTTGATTGC" "mda_day21_GGCTCGATCACCGGGT" "mda_day21_GGCTGGTCATTCCTGC" ... .. .. ..$ 7-30: chr [1:100] "mda_day21_GTGTGCGTCCGCGTTT" "mda_day21_GTGTTAGAGCAACGGT" "mda_day21_GTGTTAGGTGATAAAC" "mda_day21_GTTAAGCGTACGAAAT" ... .. .. ..$ 7-31: chr [1:100] "mda_day21_TCAGATGCAAGGACAC" "mda_day21_TCAGATGGTCCTCTTG" "mda_day21_TCAGATGGTTATGCGT" "mda_day21_TCAGATGTCTGATTCT" ... .. .. ..$ 7-32: chr [1:100] "mda_day21_TGGCTGGAGGGAAACA" "mda_day21_TGGCTGGGTGGACGAT" "mda_day21_TGGCTGGGTTAAGACA" "mda_day21_TGGCTGGTCCAATGGT" ... .. .. ..$ 7-33: chr [1:100] "mda_day28_AACCGCGGTCCGAGTC" "mda_day28_AACGTTGAGATATGCA" "mda_day28_AACTGGTAGTCAAGCG" "mda_day28_AACTGGTTCACAAACC" ... .. .. ..$ 7-34: chr [1:100] "mda_day35_AATCCAGAGAGAACAG" "mda_day35_ACTGAGTCATTTGCCC" "mda_day35_AGAGCGACAGGAATCG" "mda_day35_AGTCTTTGTAGCGCTC" ... .. .. ..$ 7-35: chr [1:100] "mda_day21_ACGCCAGAGCGGCTTC" "mda_day21_ACGGGCTAGACAATAC" "mda_day21_AGGGAGTTCCAAAGTC" "mda_day21_CAGCATAAGCGTCTAT" ... .. .. ..$ 7-36: chr [1:101] "mda_day21_ACGTCAACAACGATGG" "mda_day21_ACGTCAATCGCCTGTT" "mda_day21_ACTATCTAGCGCCTTG" "mda_day21_ACTATCTAGTTAGCGG" ... .. .. ..$ 7-37: chr [1:100] "mda_day21_GACGGCTAGACGACGT" "mda_day21_GACTACAAGCCACCTG" "mda_day21_GACTACACACGAAAGC" "mda_day21_GAGTCCGTCTGACCTC" ... .. .. ..$ 7-38: chr [1:100] "mda_day21_TGGTTCCCAAGTTCTG" "mda_day21_TGTATTCGTTGGGACA" "mda_day21_TGTGGTAAGCCTATGT" "mda_day21_TGTTCCGCAAGTAATG" ... .. .. ..$ 7-39: chr [1:100] "mda_day21_GTCGTAACAATGGAGC" "mda_day21_TACCTTAGTAGGAGTC" "mda_day21_TCAGGATTCTCAAACG" "mda_day21_TGACTTTAGGCCCTTG" ... .. .. ..$ 7-40: chr [1:100] "mda_day21_CAGGTGCTCGGTCTAA" "mda_day28_TCTTTCCCAAGTAATG" "mda_day28_ATTGGTGCATGTAGTC" "mda_day28_CGTCCATCAATAACGA" ... .. .. ..$ 7-41: chr [1:100] "mda_day21_AGCGTATCAGCGATCC" "mda_day35_CTAGCCTTCAAACCGT" "mda_day21_CACCAGGGTGTCGCTG" "mda_day21_GCTTCCACAGTAAGCG" ... .. .. ..$ 7-42: chr [1:100] "mda_day28_GGACAGACAAGAAGAG" "mda_day35_ACGCCGAAGGAGTACC" "mda_day35_GAACGGACAAGGGTCA" "mda_day21_TGACTAGAGAGGTAGA" ... .. .. ..$ 7-43: chr [1:100] "mda_day21_TATCTCACAAAGTGCG" "mda_day35_GATCTAGTCAACGCTA" "mda_day35_TCGCGAGGTAATCGTC" "mda_day21_CATGGCGGTAAGTTCC" ... .. .. ..$ 7-44: chr [1:100] "mda_day21_AGAGCGAGTGGCCCTA" "mda_day35_GATCGTATCAAACAAG" "mda_day28_GTCAAGTGTACAGTTC" "mda_day21_CATCCACCATCACGTA" ... .. .. ..$ 7-45: chr [1:100] "mda_day35_GGATGTTAGTCAAGCG" "mda_day35_GACGCGTTCGGCGCAT" "mda_day28_ACACCCTAGCTCTCGG" "mda_day21_TGTTCCGCATCTCCCA" ... .. .. ..$ 7-46: chr [1:100] "mda_day21_ACGCCGATCTGGGCCA" "mda_day21_CGTCTACGTTCGCGAC" "mda_day28_GTCGTAACATGTTGAC" "mda_day35_TGACTAGTCGGCTACG" ... .. .. ..$ 7-47: chr [1:100] "mda_day35_AGATTGCGTTTACTCT" "mda_day35_AGAATAGGTCTCCACT" "mda_day35_GTACTTTCAGTGGAGT" "mda_day21_GTACTCCAGTGTGAAT" ... .. .. ..$ 7-48: chr [1:100] "mda_day21_CAGAGAGAGGAGTAGA" "mda_day21_GCTCCTACAAAGTGCG" "mda_day21_CGGAGCTCAACGATCT" "mda_day28_CAGCATAAGCTAAGAT" ... .. .. ..$ 7-49: chr [1:100] "mda_day21_ATAAGAGGTCACAAGG" "mda_day35_AAGACCTGTCCGAATT" "mda_day21_GAACATCCATGGTTGT" "mda_day28_TGAGCATCAGTGGGAT" ... .. .. ..$ 7-50: chr [1:100] "mda_day21_TGTCCCAAGCCGGTAA" "mda_day35_GTAACGTTCGTCACGG" "mda_day28_GGTGTTACACCTATCC" "mda_day28_GAGGTGAAGTGGTAGC" ... .. .. ..$ 7-51: chr [1:100] "mda_day28_GACAGAGTCGAGGTAG" "mda_day21_GATGAAACAAGGTGTG" "mda_day28_CTGCCTAAGATATACG" "mda_day28_CACCTTGCATGGTCTA" ... .. .. ..$ 7-52: chr [1:100] "mda_day35_GATCGTAAGAGAACAG" "mda_day35_ACACCCTCAGGAACGT" "mda_day28_TTCCCAGAGCCAACAG" "mda_day35_CCCAGTTTCCGCATAA" ... .. .. ..$ 7-53: chr [1:100] "mda_day35_ACGGAGATCTGGAGCC" "mda_day21_CCTCTGAAGCCACGTC" "mda_day35_AACTTTCTCAGTGTTG" "mda_day21_CGTAGCGTCGCAAACT" ... .. .. ..$ 7-54: chr [1:100] "mda_day28_CTCACACGTCTAAAGA" "mda_day35_CTACACCAGAGTGAGA" "mda_day21_CGTAGGCGTCGAATCT" "mda_day28_CAGCGACCATACGCCG" ... .. .. ..$ 7-55: chr [1:100] "mda_day35_ACATGGTCAAGCCCAC" "mda_day21_GTACTCCCATGCTGGC" "mda_day35_GTTCTCGTCCTAGTGA" "mda_day21_GTTTCTATCTTCTGGC" ... .. .. ..$ 7-56: chr [1:100] "mda_day28_TTCTCAATCAGTTGAC" "mda_day35_CTTAGGAAGGGATCTG" "mda_day28_TACTTACTCAGTTGAC" "mda_day28_GTCACAAGTACTCTCC" ... .. .. ..$ 7-57: chr [1:100] "mda_day21_GCTTCCATCTTGCATT" "mda_day35_GCGCGATCATGCTAGT" "mda_day35_CAGCTGGGTTGAGGTG" "mda_day35_CTCCTAGAGCGTGTCC" ... .. .. ..$ 7-58: chr [1:100] "mda_day35_AGCATACCAAGCGTAG" "mda_day21_AACACGTCAAGTACCT" "mda_day35_GTTTCTATCACTTATC" "mda_day21_ATAACGCGTAGCCTCG" ... .. .. ..$ 7-59: chr [1:100] "mda_day35_TGTGTTTCAAGAGGCT" "mda_day21_TTAGTTCTCCCACTTG" "mda_day35_TGTCCCAAGACGCAAC" "mda_day21_GGTGTTACAAACGCGA" ... .. .. ..$ 7-60: chr [1:100] "mda_day35_CTCAGAACAAAGGAAG" "mda_day35_CAACCAAAGGTGTGGT" "mda_day35_TCAGCAAAGCTCAACT" "mda_day35_CGAATGTAGTGTTGAA" ... .. .. ..$ 7-61: chr [1:100] "mda_day35_CGTGTAACAGGATTGG" "mda_day21_CTGGTCTTCACTCTTA" "mda_day35_GGTGCGTGTTATGCGT" "mda_day35_ATTCTACTCCGCGGTA" ... .. .. ..$ 7-62: chr [1:100] "mda_day35_GGGACCTAGCAGACTG" "mda_day35_CAAGTTGCATGATCCA" "mda_day21_TCGCGAGTCCTAGTGA" "mda_day35_CTTGGCTTCGCCATAA" ... .. .. ..$ 7-63: chr [1:100] "mda_day35_ACGGCCAAGTTGCAGG" "mda_day35_CACAGTAAGTATCTCG" "mda_day35_GCATACACAGTCTTCC" "mda_day35_GCTTGAAGTACCGTTA" ... .. .. .. [list output truncated] .. ..$ node.mean.pseudotime : Named num [1:107] 0.268 0.276 0.284 0.292 0.299 ... .. .. ..- attr(, "names")= chr [1:107] "5-1" "5-2" "5-3" "5-4" ... .. ..$ node.max.pseudotime : Named num [1:107] 0.273 0.28 0.289 0.295 0.302 ... .. .. ..- attr(, "names")= chr [1:107] "5-1" "5-2" "5-3" "5-4" ... .. ..$ edge.list : chr [1:106, 1:2] "5-1" "5-2" "5-3" "5-4" ... .. .. ..- attr(, "dimnames")=List of 2 .. .. .. ..$ : chr [1:106] "" "" "" "" ... .. .. .. ..$ : NULL .. ..$ tree.igraph :List of 10 .. .. ..$ :List of 1 .. .. .. ..$ 7: 'igraph.vs' Named int [1:2] 2 3 .. .. .. .. ..- attr(, "names")= chr [1:2] "5" "6" .. .. .. .. ..- attr(, "env")= .. .. .. .. ..- attr(, "graph")= chr "2d51c0f4-c943-4641-b1bd-c264160f0d9b" .. .. ..$ :List of 1 .. .. .. ..$ 5: 'igraph.vs' Named int(0) .. .. .. .. ..- attr(, "names")= chr(0) .. .. .. .. ..- attr(, "env")= .. .. .. .. ..- attr(, "graph")= chr "2d51c0f4-c943-4641-b1bd-c264160f0d9b" .. .. ..$ :List of 1 .. .. .. ..$ 6: 'igraph.vs' Named int(0) .. .. .. .. ..- attr(, "names")= chr(0) .. .. .. .. ..- attr(, "env")= .. .. .. .. ..- attr(, "graph")= chr "2d51c0f4-c943-4641-b1bd-c264160f0d9b" .. .. ..$ :Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : At iterators.c:759 : Cannot create iterator, invalid vertex id, Invalid vertex id

[farrellja]

Hi @MichaelPeibo,

Is it possible that the clustering that you used for the tips had some cells that were not assigned to a cluster, and so were called Unknown? If you look at the list of tips you used with as.character(object@tree$segment.names), does it contain "Unknown"? If so, you probably don't want to use it for differential expression (or additionally, potentially don't want to use it for building your tree...)

tips.to.run <- setdiff(as.character(object@tree$segment.names), c("Unknown"))

[MichaelPeibo]

Hi @farrellja I doubt that it is due to the clustering that you used for the tips had some cells that were not assigned to a cluster, since the tips are generated by increasing resolution of clustering.

And when I do single trajectory gene cascade analysis, the error came too.

markers <-aucprTestAlongTree(urd.tree, pseudotime="pseudotime", tips='9', 
  log.effect.size=0.4, auc.factor = 1.25, max.auc.threshold = 0.85, frac.must.express = 0.1, root='11',
  frac.min.diff = 0, genes.use=genes.use, only.return.global=F, must.beat.sibs=0.6, report.debug=T)

Error in names(stats) <- c("n.1", "n.2", "pt.1.mean", "pt.2.mean", "pt.1.median", : 'names' attribute [14] must be the same length as the vector [10] In addition: Warning messages: 1: In if (format == "unary") { : the condition has length > 1 and only the first element will be used 2: In mean.default(object@meta[cells.1, "n.Genes"]) : argument is not numeric or logical: returning NA 3: In mean.default(object@meta[cells.2, "n.Genes"]) : argument is not numeric or logical: returning NA 4: In mean.default(object@meta[cells.1, "n.Trans"]) : argument is not numeric or logical: returning NA 5: In mean.default(object@meta[cells.2, "n.Trans"]) : argument is not numeric or logical: returning NA

One thing to mention, when I build the tree, I got the warning that some cells are not visited by a branch and assigned. Is it a concern?

[1] "Calculating divergence between 9 and 10 (Pseudotime 0 to 0.523)" [1] "Joining segments 9 and 10 at pseudotime 0.229 to create segment 11" [1] "Assigning cells to segments." [1] "Collapsing short segments." [1] "Removing singleton segments." [1] "Reassigning cells to segments." [1] "Assigning cells to nodes." [1] "Laying out tree." [1] "Adding cells to tree." Warning messages: 1: In assignCellsToSegments(object, pseudotime, verbose) : 221 cells were not visited by a branch that exists at their pseudotime and were not assigned. 2: In assignCellsToSegments(object, pseudotime, verbose) : 221 cells were not visited by a branch that exists at their pseudotime and were not assigned.

[farrellja]

It's not a concern that some cells are not visited; that's normal behavior.

'Unknown' does not appear in the URD codebase, so the fact that there is a tip called Unknown is coming from your object, I believe.

Can you provide me with a reproducible example? I will try to see what has gone wrong.

[MichaelPeibo]

Hi @farrellja Thanks for help! I have sent your file with Dropbox to your email shown in lab website https://www.schierlab.fas.harvard.edu/currentmembers

[MichaelPeibo]

Hi @farrellja , I checked the errors and source code of aucprTestAlongTree, I found it is the unmatched names of obj@meta for n.Genes and n.Trans, in my case, I got not the exact same names, due to the object converted from Seurat.

I have changed colnames and it works now.

Thanks for help!