Main Function Crashes: attempt to set 'colnames' on an object with less than two dimensions

[onurdanaci]

Hi,

Running the Main_Doublet_Decon function, even for the tutorial dataset, crashes the whole thing. Just following the tutorial pipeline in the github gave me the following output (error after step 3):

Step 1: Removing possible doublets...
Step 2: Re-clustering possible doublets...
Step 3: Rescuing cells with unique gene expression...
Error in colnames<-(*tmp*, value = c("clusterNr", "clusterName", "cellName")) :
attempt to set 'colnames' on an object with less than two dimensions
In addition: Warning messages:
1: In if (!is.null(v) && is.atomic(x[[jj]]) && !is.null(names(x[[jj]]))) names(x[[jj]]) <- NULL :
closing unused connection 3 (/Users/danaco/Downloads/PBMC_example.log)
2: In reclust_groups$cells <- row.names(reclust_groups) :
Coercing LHS to a list
%%%%%%%%%%%%%%%%

My configuration is:

R version 3.6.0 (2019-04-26)
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/3.6/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] stats4 grid parallel stats graphics
[6] grDevices utils datasets methods base

other attached packages:
[1] stringr_1.4.0 doParallel_1.0.14
[3] iterators_1.0.10 foreach_1.4.4
[5] R.utils_2.9.0 R.oo_1.22.0
[7] R.methodsS3_1.7.1 tidyr_0.8.3
[9] mygene_1.20.0 GenomicFeatures_1.36.4
[11] AnnotationDbi_1.46.0 GenomicRanges_1.36.0
[13] GenomeInfoDb_1.20.0 IRanges_2.18.1
[15] S4Vectors_0.22.0 clusterProfiler_3.12.0
[17] MCL_1.0 dplyr_0.8.3
[19] gplots_3.0.1.1 DeconRNASeq_1.26.0
[21] ggplot2_3.2.0 pcaMethods_1.76.0
[23] Biobase_2.44.0 BiocGenerics_0.30.0
[25] limSolve_1.5.5.3 DoubletDecon_1.0.2
[27] Seurat_3.0.2

loaded via a namespace (and not attached):
[1] proto_1.0.0
[2] reticulate_1.12
[3] tidyselect_0.2.5
[4] RSQLite_2.1.1
[5] htmlwidgets_1.3
[6] BiocParallel_1.18.0
[7] Rtsne_0.15
[8] lpSolve_5.6.13.1
[9] munsell_0.5.0
[10] codetools_0.2-16
[11] ica_1.0-2
[12] chron_2.3-53
[13] future_1.14.0
[14] withr_2.1.2
[15] colorspace_1.4-1
[16] GOSemSim_2.10.0
[17] knitr_1.23
[18] rstudioapi_0.10
[19] ROCR_1.0-7
[20] DOSE_3.10.2
[21] gbRd_0.4-11
[22] listenv_0.7.0
[23] Rdpack_0.11-0
[24] urltools_1.7.3
[25] GenomeInfoDbData_1.2.1
[26] polyclip_1.10-0
[27] bit64_0.9-7
[28] farver_1.1.0
[29] vctrs_0.2.0
[30] xfun_0.8
[31] R6_2.4.0
[32] rsvd_1.0.1
[33] bitops_1.0-6
[34] fgsea_1.10.0
[35] gridGraphics_0.4-1
[36] DelayedArray_0.10.0
[37] assertthat_0.2.1
[38] SDMTools_1.1-221.1
[39] scales_1.0.0
[40] ggraph_1.0.2
[41] nnet_7.3-12
[42] enrichplot_1.4.0
[43] gtable_0.3.0
[44] npsurv_0.4-0
[45] globals_0.12.4
[46] rlang_0.4.0
[47] zeallot_0.1.0
[48] splines_3.6.0
[49] rtracklayer_1.44.2
[50] lazyeval_0.2.2
[51] acepack_1.4.1
[52] europepmc_0.3
[53] checkmate_1.9.4
[54] reshape2_1.4.3
[55] backports_1.1.4
[56] qvalue_2.16.0
[57] Hmisc_4.2-0
[58] tools_3.6.0
[59] ggplotify_0.0.3
[60] RColorBrewer_1.1-2
[61] ggridges_0.5.1
[62] gsubfn_0.7
[63] Rcpp_1.0.1
[64] plyr_1.8.4
[65] base64enc_0.1-3
[66] progress_1.2.2
[67] zlibbioc_1.30.0
[68] purrr_0.3.2
[69] RCurl_1.95-4.12
[70] prettyunits_1.0.2
[71] rpart_4.1-15
[72] sqldf_0.4-11
[73] pbapply_1.4-1
[74] viridis_0.5.1
[75] cowplot_1.0.0
[76] zoo_1.8-6
[77] SummarizedExperiment_1.14.0
[78] ggrepel_0.8.1
[79] cluster_2.1.0
[80] magrittr_1.5
[81] data.table_1.12.2
[82] DO.db_2.9
[83] lmtest_0.9-37
[84] triebeard_0.3.0
[85] RANN_2.6.1
[86] fitdistrplus_1.0-14
[87] matrixStats_0.54.0
[88] hms_0.5.0
[89] lsei_1.2-0
[90] XML_3.98-1.20
[91] gridExtra_2.3
[92] compiler_3.6.0
[93] biomaRt_2.40.3
[94] tibble_2.1.3
[95] KernSmooth_2.23-15
[96] crayon_1.3.4
[97] htmltools_0.3.6
[98] Formula_1.2-3
[99] expm_0.999-4
[100] DBI_1.0.0
[101] tweenr_1.0.1
[102] MASS_7.3-51.4
[103] Matrix_1.2-17
[104] quadprog_1.5-7
[105] gdata_2.18.0
[106] metap_1.1
[107] igraph_1.2.4.1
[108] pkgconfig_2.0.2
[109] rvcheck_0.1.3
[110] GenomicAlignments_1.20.1
[111] foreign_0.8-71
[112] plotly_4.9.0
[113] xml2_1.2.0
[114] XVector_0.24.0
[115] bibtex_0.4.2
[116] digest_0.6.20
[117] sctransform_0.2.0
[118] tsne_0.1-3
[119] Biostrings_2.52.0
[120] fastmatch_1.1-0
[121] htmlTable_1.13.1
[122] Rsamtools_2.0.0
[123] gtools_3.8.1
[124] nlme_3.1-140
[125] jsonlite_1.6
[126] viridisLite_0.3.0
[127] pillar_1.4.2
[128] lattice_0.20-38
[129] httr_1.4.0
[130] survival_2.44-1.1
[131] GO.db_3.8.2
[132] glue_1.3.1
[133] UpSetR_1.4.0
[134] png_0.1-7
[135] bit_1.1-14
[136] ggforce_0.2.2
[137] stringi_1.4.3
[138] blob_1.2.0
[139] latticeExtra_0.6-28
[140] caTools_1.17.1.2
[141] memoise_1.1.0
[142] irlba_2.3.3
[143] future.apply_1.3.0
[144] ape_5.3

[EDePasquale]

This issue should be corrected now. Seurat_Pre_Process outputs a matrix but the command line version of DoubletDecon expects a data.frame. The UI version, however, needs a matrix format so I convert to data.frame internally when it is needed in the command line version. Please let me know if this or other problems persist.