rcorces
commented
1 year ago Hi @EEEleanor! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
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Hello, I'm calculating the co-accessibility of a specified cell type using addCoAccessibility with 'cellsToUse'. However, there is no output of , and no error is reported in the log. Could you please help me find the solution? Thank you so much!
ArchR-addCoAccessibility-7567632ab962-Date-2023-05-16_Time-23-20-48.log
My code is: projHeme5 <- addCoAccessibility( ArchRProj = projHeme5, reducedDims = "IterativeLSI", cellsToUse =rownames(projHeme5@cellColData[which(projHeme5@cellColData$celltypes==celltype),]) )
When I use cA <- getCoAccessibility( ArchRProj = projHeme5, corCutOff = 0.2, resolution = 1, returnLoops = FALSE ) to extract co-accessibility results, there was nothing in cA.
This situation only happened in using parameter 'cellsToUse '. After removing 'cellsToUse ', the output is normal.
Session Info sessionInfo()
R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /p300s/biosoft/app/python/python3.9/envs/R4.1.3/lib/libmkl_rt.so.2
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 grid stats graphics grDevices utils [8] datasets methods base
other attached packages: [1] nabor_0.5.0 ggrepel_0.9.1 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.62.0 [5] rtracklayer_1.54.0 Biostrings_2.62.0 [7] XVector_0.34.0 rhdf5_2.38.0 [9] SummarizedExperiment_1.24.0 Biobase_2.54.0 [11] MatrixGenerics_1.6.0 Rcpp_1.0.10 [13] Matrix_1.4-1 GenomicRanges_1.46.1 [15] GenomeInfoDb_1.30.0 IRanges_2.28.0 [17] S4Vectors_0.32.3 BiocGenerics_0.40.0 [19] matrixStats_0.62.0 data.table_1.14.8 [21] stringr_1.5.0 plyr_1.8.7 [23] magrittr_2.0.3 ggplot2_3.3.6 [25] gtable_0.3.0 gtools_3.9.2 [27] gridExtra_2.3 ArchR_1.0.2
loaded via a namespace (and not attached): [1] lattice_0.20-45 Rsamtools_2.10.0 digest_0.6.29 [4] utf8_1.2.3 R6_2.5.1 pillar_1.9.0 [7] zlibbioc_1.40.0 rlang_1.1.1 labeling_0.4.2 [10] BiocParallel_1.28.3 RCurl_1.98-1.6 munsell_0.5.0 [13] DelayedArray_0.20.0 compiler_4.1.3 pkgconfig_2.0.3 [16] tidyselect_1.2.0 tibble_3.2.1 GenomeInfoDbData_1.2.7 [19] codetools_0.2-18 XML_3.99-0.9 fansi_1.0.4 [22] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0 [25] GenomicAlignments_1.30.0 rhdf5filters_1.6.0 bitops_1.0-7 [28] lifecycle_1.0.3 scales_1.2.1 cli_3.6.1 [31] stringi_1.7.6 farver_2.1.0 generics_0.1.3 [34] vctrs_0.6.2 Rhdf5lib_1.16.0 rjson_0.2.21 [37] restfulr_0.0.13 tools_4.1.3 Cairo_1.6-0 [40] glue_1.6.2 yaml_2.3.5 colorspace_2.0-3 [43] BiocIO_1.4.0