Closed ahorn720 closed 3 years ago
LiNk-NY
commented
3 years ago Hi @ahorn720,
Can you provide a minimally reproducible example?
Also, what is the return of BiocManager;:valid() and BiocManager::version()?
I would recommend you use makeGRangesFromDataFrame.
ahorn720
commented
3 years ago Thank you for the quick response. I spent far tooo long trying to figure this out. I’ve attached the cna dataframe from the op.
Let me know if you need me to send it in a different format though.
Here is the code I was running which gave me the error: gr <- GRanges(seqnames=paste0("chr",cna$chrom), ranges=IRanges(cna$loc.start, cna$loc.end), strand="*”)
gr <- GRanges(seqnames=paste0("chr",cna$chrom),
- ranges=IRanges(cna$loc.start,
- cna$loc.end),
- strand="*") # Turn intoo GRanges object gr GRanges object with 125 ranges and 0 metadata columns: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
BiocManager::version() [1] ‘3.11’
I’ve attached the bcocmanager::valid() output.
Thank you!
Aaron
On Nov 16, 2020, at 6:25 PM, Marcel Ramos notifications@github.com wrote:
Hi @ahorn720 https://github.com/ahorn720, Can you provide a minimally reproducible example? Also, what is the return of BiocManager;:valid() and BiocManager::version()? I would recommend you use makeGRangesFromDataFrame.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/GenomicRanges/issues/47#issuecomment-728644734, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY3HYZY47XJPQRYH5FP7VDSQHNLBANCNFSM4TX3PZMQ.
LiNk-NY
commented
3 years ago Hi Aaron, @ahorn720
AFAIK attaching files does not work if you're responding via email.
Please post the reproducible example here using reprex::reprex.
If you have a small dataset to share, try using either dput or a data.frame() call
in the reprex.
I would recommend that you update your R version to >= 4.0.
My hunch is that there is an issue with the data rather than GenomicRanges
which is a pretty robust package. I'm looking forward to the reproducible
example.
Best, Marcel
ahorn720
commented
3 years ago Oh! I didn't see that this was on the GitHub thread! My apologies.
Well after I ran the BiocManager::valid() and saw that there was a recommended install, I ran that and refreshed the R session and now the code works.
library(GenomicRanges)
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:parallel':
#>
#> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#> clusterExport, clusterMap, parApply, parCapply, parLapply,
#> parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#> union, unique, unsplit, which, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:base':
#>
#> expand.grid
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
cna = readr::read_rds("~/Desktop/cna_sample.rds")
head(cna,20)
#> chrom loc.start loc.end num.mark seg.mean copynumber minor_cn major_cn
#> 1 1 1 60278618 38700 0.013 2 1 1
#> 2 1 60278619 60280056 1 0.100 6 1 5
#> 3 1 60280057 122661020 46080 -0.019 2 1 1
#> 4 1 122661021 124971287 117 0.077 3 1 2
#> 5 1 124971288 125073244 78 0.006 2 1 1
#> 6 1 125073245 125116434 5 0.026 4 1 3
#> 7 1 125116435 234775098 53820 -0.006 2 1 1
#> 8 1 234775099 234802730 26 -0.023 3 1 2
#> 9 1 234802731 248956422 7841 0.008 2 1 1
#> 10 2 1 89349774 61171 -0.005 2 1 1
#> 11 2 89349775 94340332 307 0.071 3 1 2
#> 12 2 94340333 242193529 90515 -0.009 2 1 1
#> 13 3 1 90718825 65206 -0.008 2 1 1
#> 14 3 90718826 91226754 43 0.212 3 1 2
#> 15 3 91226755 188755202 63592 -0.013 2 1 1
#> 16 3 188755203 188756456 1 0.200 7 1 6
#> 17 3 188756457 195646798 5708 -0.011 2 1 1
#> 18 3 195646799 195723594 76 0.032 3 1 2
#> 19 3 195723595 198295559 1838 0.011 2 1 1
#> 20 4 1 49363652 33206 -0.006 2 1 1
#> allelicratio LOHcall cellularprevalence ploidy normalproportion
#> 1 0.580 HET NA 2.004 0
#> 2 0.970 ASCNA 1 2.004 0
#> 3 0.583 HET NA 2.004 0
#> 4 0.715 GAIN 1 2.004 0
#> 5 0.586 HET NA 2.004 0
#> 6 0.826 ASCNA 1 2.004 0
#> 7 0.582 HET NA 2.004 0
#> 8 0.719 GAIN 1 2.004 0
#> 9 0.582 HET NA 2.004 0
#> 10 0.582 HET NA 2.004 0
#> 11 0.712 GAIN 1 2.004 0
#> 12 0.583 HET NA 2.004 0
#> 13 0.583 HET NA 2.004 0
#> 14 0.697 GAIN 1 2.004 0
#> 15 0.583 HET NA 2.004 0
#> 16 0.970 ASCNA 1 2.004 0
#> 17 0.583 HET NA 2.004 0
#> 18 0.735 GAIN 1 2.004 0
#> 19 0.582 HET NA 2.004 0
#> 20 0.582 HET NA 2.004 0
#> logcopynumberratio seg.mean.adj
#> 1 0.000 0.016
#> 2 1.585 0.103
#> 3 0.000 -0.016
#> 4 0.585 0.080
#> 5 0.000 0.009
#> 6 1.000 0.029
#> 7 0.000 -0.003
#> 8 0.585 -0.020
#> 9 0.000 0.011
#> 10 0.000 -0.002
#> 11 0.585 0.074
#> 12 0.000 -0.006
#> 13 0.000 -0.005
#> 14 0.585 0.215
#> 15 0.000 -0.010
#> 16 1.807 0.203
#> 17 0.000 -0.008
#> 18 0.585 0.035
#> 19 0.000 0.014
#> 20 0.000 -0.003
gr <- GRanges(seqnames=cna$chrom,
ranges=IRanges(cna$loc.start,
cna$loc.end),
strand="*") # Turn intoo GRanges object
gr
#> GRanges object with 125 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] 1 1-60278618 *
#> [2] 1 60278619-60280056 *
#> [3] 1 60280057-122661020 *
#> [4] 1 122661021-124971287 *
#> [5] 1 124971288-125073244 *
#> ... ... ... ...
#> [121] 21 12985089-46709983 *
#> [122] 22 1-11298106 *
#> [123] 22 11298107-11462963 *
#> [124] 22 11462964-15965511 *
#> [125] 22 15965512-50818468 *
#> -------
#> seqinfo: 22 sequences from an unspecified genome; no seqlengths
BiocManager::valid()
#> Warning: 1 packages out-of-date; 1 packages too new
#>
#> * sessionInfo()
#>
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.7
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] parallel stats4 stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2
#> [4] S4Vectors_0.26.1 BiocGenerics_0.34.0
#>
#> loaded via a namespace (and not attached):
#> [1] knitr_1.30 XVector_0.28.0 magrittr_1.5
#> [4] hms_0.5.3 zlibbioc_1.34.0 R6_2.5.0
#> [7] rlang_0.4.8 stringr_1.4.0 highr_0.8
#> [10] tools_4.0.2 xfun_0.19 ellipsis_0.3.1
#> [13] htmltools_0.5.0 yaml_2.2.1 digest_0.6.27
#> [16] tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4
#> [19] GenomeInfoDbData_1.2.3 BiocManager_1.30.10 readr_1.4.0
#> [22] vctrs_0.3.4 fs_1.5.0 bitops_1.0-6
#> [25] RCurl_1.98-1.2 evaluate_0.14 rmarkdown_2.5
#> [28] reprex_0.3.0.9001 stringi_1.5.3 pillar_1.4.6
#> [31] compiler_4.0.2 pkgconfig_2.0.3
#>
#> Bioconductor version '3.11'
#>
#> * 1 packages out-of-date
#> * 1 packages too new
#>
#> create a valid installation with
#>
#> BiocManager::install(c(
#> "RcppArmadillo", "reprex"
#> ), update = TRUE, ask = FALSE)
#>
#> more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_dateCreated on 2020-11-16 by the reprex package (v0.3.0.9001)
I think it had something to do with IRanges needing to be updated or something.
Thank you very much for guiding me towards the answer!
ahorn720
commented
3 years ago and for introducing me to reprex::reprex()! very cool
LiNk-NY
commented
3 years ago Hi Aaron, @ahorn720
I'm glad it worked out!
Note. I would still use makeGRangesFromDataFrame possibly with keep.extra.columns=TRUE to not lose any data.
Also, RaggedExperiment for representing multiple samples with 'ragged' measurements.
Best,
Marcel
Im trying to create a Granges object from a data frame. Here is my data frame:
I can make a a Granges object with 11 rows:
but once I add another row, up to 12, it throws an error:
Im only showing a small portion of the larger problem...I want to make the first 3 columns of
cnainto a Granges object but I found that these row errors were happening.