load_cellranger_data Error

[sunil1learn]

Hi, I am having trouble in import cell ranger 3 data in Monocle3. Earlier cell ranger 2 was working fine with Monocle2 library. load_cellranger_data is not working. Error: object 'load_cellranger_matrix' not found. Please see below my session info.

R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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 methods base

other attached packages: [1] monocle_2.99.3 L1Graph_0.1.1 lpSolveAPI_5.5.2.0-17 DDRTree_0.1.5
[5] irlba_2.3.3 igraph_1.2.4 ggplot2_3.1.0 Biobase_2.42.0
[9] DelayedArray_0.8.0 BiocParallel_1.16.6 IRanges_2.16.0 S4Vectors_0.20.1
[13] BiocGenerics_0.28.0 matrixStats_0.54.0 Matrix_1.2-15

loaded via a namespace (and not attached): [1] Rtsne_0.15 VGAM_1.1-1 colorspace_1.4-0 deldir_0.1-16
[5] class_7.3-15 rprojroot_1.3-2 fs_1.2.6 rstudioapi_0.9.0
[9] listenv_0.7.0 remotes_2.0.2 ggrepel_0.8.0 codetools_0.2-16
[13] splines_3.5.2 docopt_0.6.1 doParallel_1.0.14 knitr_1.21
[17] pkgload_1.0.2 jsonlite_1.6 cluster_2.0.7-1 pheatmap_1.0.12
[21] shiny_1.2.0 compiler_3.5.2 httr_1.4.0 backports_1.1.3
[25] assertthat_0.2.0 lazyeval_0.2.1 limma_3.38.3 cli_1.0.1
[29] later_0.8.0 htmltools_0.3.6 prettyunits_1.0.2 tools_3.5.2
[33] coda_0.19-2 gtable_0.2.0 glue_1.3.0 RANN_2.6.1
[37] reshape2_1.4.3 dplyr_0.8.0.1 gmodels_2.18.1 Rcpp_1.0.0
[41] slam_0.1-44 spdep_1.0-2 gdata_2.18.0 nlme_3.1-137
[45] iterators_1.0.10 crosstalk_1.0.0 xfun_0.5 stringr_1.4.0
[49] globals_0.12.4 ps_1.3.0 mime_0.6 miniUI_0.1.1.1
[53] gtools_3.8.1 devtools_2.0.1 future_1.11.1.1 LearnBayes_2.15.1
[57] MASS_7.3-51.1 scales_1.0.0 promises_1.0.1 expm_0.999-3
[61] RColorBrewer_1.1-2 memoise_1.1.0 pbapply_1.4-0 gridExtra_2.3
[65] fastICA_1.2-1 stringi_1.3.1 desc_1.2.0 foreach_1.4.4
[69] e1071_1.7-0.1 boot_1.3-20 densityClust_0.3 pkgbuild_1.0.2
[73] manipulateWidget_0.10.0 spData_0.3.0 rlang_0.3.1 pkgconfig_2.0.2
[77] rgl_0.99.16 qlcMatrix_0.9.7 lattice_0.20-38 purrr_0.3.0
[81] sf_0.7-3 htmlwidgets_1.3 processx_3.2.1 tidyselect_0.2.5
[85] plyr_1.8.4 magrittr_1.5 R6_2.4.0 DBI_1.0.0
[89] pillar_1.3.1 withr_2.1.2 units_0.6-2 sp_1.3-1
[93] tibble_2.0.1 crayon_1.3.4 plotly_4.8.0 viridis_0.5.1
[97] usethis_1.4.0 grid_3.5.2 data.table_1.12.0 FNN_1.1.3
[101] callr_3.1.1 HSMMSingleCell_1.2.0 sparsesvd_0.1-4 digest_0.6.18
[105] classInt_0.3-1 webshot_0.5.1 pbmcapply_1.3.1 xtable_1.8-3
[109] tidyr_0.8.2 httpuv_1.4.5.1 munsell_0.5.0 glmnet_2.0-16
[113] viridisLite_0.3.0 sessioninfo_1.1.1

[evolvedmicrobe]

The function to use is now called load_cellranger_data, I'd give that a try.

[sunil1learn]

I am getting Error: object 'load_cellranger_matrix' not found.

[sunil1learn]

?load_cellranger_data No documentation for ‘load_cellranger_data’ in specified packages and libraries: you could try ‘??load_cellranger_data’

[sunil1learn]

?load_cellranger_data() Error in .helpForCall(topicExpr, parent.frame()) : no methods for ‘load_cellranger_data’ and no documentation for it as a function

[evolvedmicrobe]

Ah, I think it's a problem generating the documentation, one second

[evolvedmicrobe]

So the issue is that the branch you are using does not contain the code to load cellranger data, you'd have to use the old branch. I also found a typo in the documentation on that branch, but it won't explain your problem.

[sunil1learn]

branch means? Could you please provide the link of old branch.

[evolvedmicrobe]

Git has a concept of branches, which are different versions of the related code. Based on your sessionInfo, you've installed code from the monocle3_alpha branch.

https://github.com/cole-trapnell-lab/monocle-release/tree/monocle3_alpha

Whereas the functions to load cellranger data are only available on the master branch

https://github.com/cole-trapnell-lab/monocle-release/tree/master

To install that other branch, you can do the following:

install.packages("devtools")
library(devtools)
install_github("cole-trapnell-lab/monocle-release")

But you may then be missing some features available in the 3.0 release

[sunil1learn]

Got it. Thank you very much for your help. Appreciated.

[Xiaojieqiu]

thanks @evolvedmicrobe! we will integrate this function to our next monocle 3 release soon

[evolvedmicrobe]

@Xiaojieqiu not a problem at all! I opened up a couple PRs to fix the typo on the master branch and also add that functionality into the new 3.0 branch.

[EvoMedLab]

I have loaded the most current version of monocle via Bioconductor, and have a similar issue:

cellranger_pipestance_path <- "/data1/melanoma_scRNA/ALL" cell_data <- load_cellranger_data(cellranger_pipestance_path)

Error in load_cellranger_data(cellranger_pipestance_path) : could not find function "load_cellranger_data"

Do I need to change the version of monocle to use this function, @evolvedmicrobe ?

[evolvedmicrobe]

If your sessionInfo says monocle_2.99.3, then yes.