pairwise comparison of chromVAR deviation #954
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yxiao832
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Questions / Documentation
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This almost definitely is not an ArchR problem and is likely an environment problem. Maybe related to limited memory available. |
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I just re-run my old ArchR object which worked before. I am able to get result with my old ArchR object but not the new object. Possibly something to do with my new object? I tried
and I got Not sure what was wrong. |
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Hi ArchR team,
I asked a similar questions about 1 year ago #340.
By running
diffMotif <- getMarkerFeatures(
ArchRProj = proj,
testMethod = "wilcoxon",
useGroups = "ClusterA",
bgdGroups = "ClusterB",
binarize = FALSE,
useMatrix = "MotifMatrix",
groupBy = "Clusters",
useSeqnames="deviations"
)
This run used to take about 1 minute and I was able to get the mean diff and FDR.
However, I was trying to run this command again yesterday and waited for several hours and nothing was returned.
Log file is as below. Wondering if you have any thought what could be wrong?
Thank you!
Yang
------- ArchR Info
ArchRThreads = 16
ArchRGenome = Mm10
------- System Info
Computer OS = unix
Total Cores = 80
------- Session Info
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /gpfs/fs02/apps/R/3.5.1/lib64/R/lib/libRblas.so
LAPACK: /gpfs/fs02/apps/R/3.5.1/lib64/R/lib/libRlapack.so
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 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] chromVAR_1.4.1 ggrastr_0.1.7
[3] Cairo_1.5-12 ArchR_1.0.0
[5] magrittr_1.5 rhdf5_2.26.2
[7] Matrix_1.2-18 data.table_1.13.2
[9] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[11] BiocParallel_1.16.6 matrixStats_0.57.0
[13] Biobase_2.42.0 GenomicRanges_1.34.0
[15] GenomeInfoDb_1.18.2 IRanges_2.16.0
[17] S4Vectors_0.20.1 BiocGenerics_0.28.0
[19] ggplot2_3.3.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 DirichletMultinomial_1.24.1
[3] TFBSTools_1.20.0 bit64_0.9-7
[5] httr_1.4.1 repr_1.1.0
[7] tools_3.5.1 R6_2.4.1
[9] DT_0.13 lazyeval_0.2.2
[11] seqLogo_1.48.0 DBI_1.1.0
[13] colorspace_1.4-1 withr_2.2.0
[15] tidyselect_1.0.0 bit_1.1-15.2
[17] compiler_3.5.1 BSgenome.Mmusculus.UCSC.mm10_1.4.0
[19] plotly_4.9.2.1 rtracklayer_1.42.2
[21] caTools_1.17.1.2 scales_1.1.0
[23] readr_1.3.1 pbdZMQ_0.3-3
[25] stringr_1.4.0 digest_0.6.25
[27] Rsamtools_1.34.1 R.utils_2.9.2
[29] XVector_0.22.0 base64enc_0.1-3
[31] pkgconfig_2.0.3 htmltools_0.4.0
[33] fastmap_1.0.1 BSgenome_1.50.0
[35] htmlwidgets_1.5.1 rlang_0.4.6
[37] RSQLite_2.2.0 VGAM_1.1-3
[39] shiny_1.4.0.2 jsonlite_1.6.1
[41] gtools_3.8.2 R.oo_1.23.0
[43] dplyr_0.8.5 RCurl_1.98-1.1
[45] GO.db_3.7.0 GenomeInfoDbData_1.2.0
[47] Rcpp_1.0.5 IRkernel_1.1
[49] munsell_0.5.0 Rhdf5lib_1.4.3
[51] R.methodsS3_1.8.0 lifecycle_0.2.0
[53] stringi_1.4.6 zlibbioc_1.28.0
[55] plyr_1.8.6 grid_3.5.1
[57] blob_1.2.1 promises_1.1.0
[59] crayon_1.3.4 miniUI_0.1.1.1
[61] CNEr_1.18.1 lattice_0.20-41
[63] IRdisplay_0.7.0 Biostrings_2.50.2
[65] splines_3.5.1 annotate_1.60.1
[67] KEGGREST_1.22.0 hms_0.5.3
[69] pillar_1.4.3 uuid_0.1-4
[71] reshape2_1.4.4 TFMPvalue_0.0.8
[73] XML_3.99-0.3 glue_1.4.0
[75] evaluate_0.14 png_0.1-7
[77] vctrs_0.2.4 httpuv_1.5.2
[79] tidyr_1.0.2 gtable_0.3.0
[81] poweRlaw_0.70.4 purrr_0.3.4
[83] assertthat_0.2.1 mime_0.9
[85] xtable_1.8-4 later_1.0.0
[87] viridisLite_0.3.0 tibble_3.0.1
[89] GenomicAlignments_1.18.1 AnnotationDbi_1.44.0
[91] memoise_1.1.0 ellipsis_0.3.0
------- Log Info
2021-08-03 10:46:33 : Input-Parameters, Class = list
Input-Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
Input-Parameters$ArchRProj: length = 1
Input-Parameters$groupBy: length = 1
[1] "predictedGroup"
Input-Parameters$useGroups: length = 1
[1] "Stellate2"
Input-Parameters$bgdGroups: length = 1
[1] "Stellate1"
Input-Parameters$useMatrix: length = 1
[1] "ChromVARMatrix_cisbp"
Input-Parameters$bias: length = 2
[1] "TSSEnrichment" "log10(nFrags)"
Input-Parameters$normBy: length = 0
NULL
Input-Parameters$testMethod: length = 1
[1] "wilcoxon"
Input-Parameters$maxCells: length = 1
[1] 500
Input-Parameters$scaleTo: length = 1
[1] 10000
Input-Parameters$threads: length = 1
[1] 16
Input-Parameters$k: length = 1
[1] 100
Input-Parameters$bufferRatio: length = 1
[1] 0.8
Input-Parameters$binarize: length = 1
[1] FALSE
Input-Parameters$useSeqnames: length = 1
[1] "deviations"
Input-Parameters$verbose: length = 1
[1] TRUE
Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-getMarkerFeatures-28f37423e0746-Date-2021-08-03_Time-10-46-33.log"
Input-Parameters$ArchRProj: length = 1
Input-Parameters$groupBy: length = 1
[1] "predictedGroup"
Input-Parameters$useGroups: length = 1
[1] "Stellate2"
Input-Parameters$bgdGroups: length = 1
[1] "Stellate1"
Input-Parameters$useMatrix: length = 1
[1] "ChromVARMatrix_cisbp"
Input-Parameters$bias: length = 2
[1] "TSSEnrichment" "log10(nFrags)"
Input-Parameters$normBy: length = 0
NULL
Input-Parameters$testMethod: length = 1
[1] "wilcoxon"
Input-Parameters$maxCells: length = 1
[1] 500
Input-Parameters$scaleTo: length = 1
[1] 10000
Input-Parameters$threads: length = 1
[1] 16
Input-Parameters$k: length = 1
[1] 100
Input-Parameters$bufferRatio: length = 1
[1] 0.8
Input-Parameters$binarize: length = 1
[1] FALSE
Input-Parameters$useSeqnames: length = 1
[1] "deviations"
Input-Parameters$verbose: length = 1
[1] TRUE
Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-getMarkerFeatures-28f37423e0746-Date-2021-08-03_Time-10-46-33.log"
2021-08-03 10:46:33 : FeaturesPerSeqnames, Class = integer
FeaturesPerSeqnames: length = 2
[1] 884 884
2021-08-03 10:46:33 : FeatureDF, Class = DataFrame
DataFrame with 1768 rows and 3 columns
seqnames idx name
1 deviations 1 Tcfap2a_1
2 deviations 2 Tcfap2b_2
3 deviations 3 Tcfap2c_3
4 deviations 4 Tcfap2e_4
5 deviations 5 Tcfap2d_5
... ... ... ...
1764 z 880 Foxm1_880
1765 z 881 Mixl1_881
1766 z 882 Mef2b_882
1767 z 883 Smad5_883
1768 z 884 Smad9_884
2021-08-03 10:46:33 :
2021-08-03 10:46:33 : Matching Known Biases, 0.002 mins elapsed.
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