RcisTarget row.names issue

[jk86754]

Hi,

I am running into the following error message:

runSCENIC_2_createRegulons(scenicOptions) 09:00 Step 2. Identifying regulons tfModulesSummary:

top5perTarget top10perTarget w005 top50 top50perTarget 198 531 870 944 1254 w001 1323 09:00 RcisTarget: Calculating AUC Scoring database: [Source file: mm9-500bp-upstream-7species.mc9nr.feather] Scoring database: [Source file: mm9-tss-centered-10kb-7species.mc9nr.feather] 10:02 RcisTarget: Adding motif annotation Number of motifs in the initial enrichment: 2080070 Number of motifs annotated to the corresponding TF: 17945 10:09 RcisTarget: Prunning targets [1] "error in running command" Number of motifs that support the regulons: 17945 Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed Calls: runSCENIC_2_createRegulons ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- In addition: Warning message: non-unique values when setting 'row.names':

sessionInfo()

R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)

Matrix products: default BLAS: /sc/wo/app/R/v3.5.0/lib64/R/lib/libRblas.so LAPACK: /sc/wo/app/R/v3.5.0/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] SingleCellExperiment_1.2.0 SummarizedExperiment_1.10.1 [3] DelayedArray_0.6.1 BiocParallel_1.14.1 [5] matrixStats_0.53.1 Biobase_2.40.0 [7] GenomicRanges_1.32.3 GenomeInfoDb_1.16.0 [9] IRanges_2.14.10 S4Vectors_0.18.3 [11] BiocGenerics_0.26.0 RColorBrewer_1.1-2 [13] foreach_1.4.4 AUCell_1.2.4 [15] RcisTarget_1.0.2 SCENIC_0.99.0-03

loaded via a namespace (and not attached): [1] lattice_0.20-35 htmltools_0.3.6 blob_1.1.1 [4] XML_3.98-1.11 rlang_0.2.1 R.oo_1.22.0 [7] later_0.7.3 pillar_1.2.3 DBI_1.0.0 [10] R.utils_2.6.0 bit64_0.9-7 GenomeInfoDbData_1.1.0 [13] zlibbioc_1.26.0 R.methodsS3_1.7.1 codetools_0.2-15 [16] memoise_1.1.0 httpuv_1.4.4.1 AnnotationDbi_1.42.1 [19] GSEABase_1.42.0 Rcpp_0.12.17 xtable_1.8-2 [22] promises_1.0.1 feather_0.3.1 graph_1.58.0 [25] annotate_1.58.0 XVector_0.20.0 mime_0.5 [28] bit_1.1-14 hms_0.4.2 digest_0.6.15 [31] shiny_1.1.0 grid_3.5.0 tools_3.5.0 [34] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.10 [37] RSQLite_2.1.1 tibble_1.4.2 pkgconfig_2.0.1 [40] Matrix_1.2-14 data.table_1.11.4 iterators_1.0.9 [43] R6_2.2.2 compiler_3.5.0

Any help would be appreciated!

Joe

[s-aibar]

Hello,

I would need some more information to try to narrow down where the error might be occurring. Would you mind sending me an e-mail(sara.aibar at kuleuven.be)? It would be easier that way...

If you prefer to have a look yourself, I just uploaded the tutoral for step2 this afternoon. The first thing would be to check whether the motif enrichment is done correctly (it seems the first error happened when trying to save it as html):

` motifEnrichment_selfMotifs_wGenes <- readRDS("int/2.4_motifEnrichment_selfMotifs_wGenes.Rds")

motifEnrichment_selfMotifs_wGenes[order(motifEnrichment_selfMotifs_wGenes$NES,decreasing=TRUE),][1:5,(1:ncol(motifEnrichment_selfMotifs_wGenes)-1), with=F] `

[jk86754]

I sent you an email.

[wurentian]

I am having a very similar issue.

runSCENIC_2_createRegulons(scenicOptions) 23:08 Step 2. Identifying regulons tfModulesSummary: top5perTarget w005 top10perTarget top50perTarget top50 w001 161 226 281 882 1137 1220 23:08 RcisTarget: Calculating AUC Scoring database: [Source file: hg19-500bp-upstream-7species.mc9nr.feather] Scoring database: [Source file: hg19-tss-centered-10kb-7species.mc9nr.feather] 00:54 RcisTarget: Adding motif annotation Number of motifs in the initial enrichment: 1568977 Number of motifs annotated to the corresponding TF: 11013 01:01 RcisTarget: Prunning targets Number of motifs that support the regulons: 11013 Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning messages: 1: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 2: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 3: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 4: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 5: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 6: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 7: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 8: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 9: non-unique values when setting 'row.names': ‘ABCF2MATR3’, ‘ACO1RGS5’, ‘ADNPRGS5’, ‘AFF4MATR3’, ‘AFF4RGS5’, ‘AGGF1RGS5’, ‘AHCTF1MATR3’, ‘AKR1A1MATR3’, ‘ALX1MATR3’, ‘ANXA11MATR3’, ‘ANXA11RGS5’, ‘APEX1MATR3’, ‘APEX1RGS5’, ‘APEX2RGS5’, ‘ARRGS5’, ‘ARG2RGS5’, ‘ARNTRGS5’, ‘ARNT2RGS5’, ‘ASCC1RGS5’, ‘ASH2LRGS5’, ‘ASPSCR1MATR3’, ‘ASPSCR1RGS5’, ‘ATF2MATR3’, ‘ATF4MATR3’, ‘ATF4RGS5’, ‘ATF6BMATR3’, ‘ATF6BRGS5’, ‘ATF7RGS5’, ‘ATOH8RGS5’, ‘BADMATR3’, ‘BATFMATR3’, ‘BATFRGS5’, ‘BAXMATR3’, ‘BAXRGS5’, ‘BBXMATR3’, ‘BBXRGS5’, ‘BCLAF1MATR3’, ‘BDP1MATR3’, ‘BHLHE22MATR3’, ‘BHLHE41MATR3’, ‘BHLHE41RGS5’, ‘BNC2MATR3’, ‘BNC2RGS5’, ‘BPTFMATR3’, ‘BPTFRGS5’, ‘BRF2MATR3’, ‘CANXMATR3’, ‘CANXRGS5’, ‘CBX3MATR3’, ‘CBX3RGS5’, ‘ [... truncated]

And when I do

motifEnrichment_selfMotifs_wGenes[order(motifEnrichment_selfMotifs_wGenes$NES,decreasing=TRUE),][1:5,(1:ncol(motifEnrichment_selfMotifs_wGenes)-1), with=F] motifDb geneSet motif NES AUC highlightedTFs TFinDB TF_highConf 1: 10kb E2F1_top50 transfac_proM00920 18.2 0.421 E2F1 ** E2F1; E2F3; E2F4; E2F7; TFDP1 (directAnnotation). 2: 10kb E2F1_top50 transfac_proM00918 18.0 0.417 E2F1 * E2F1; E2F3; E2F4; TFDP1 (directAnnotation). 3: 10kb E2F1_top50 homer__TTCGCGCGAAAA_E2F 17.9 0.415 E2F1
4: 10kb E2F1_top50 cisbpM3134 17.8 0.413 E2F1 ** E2F1 (directAnnotation). 5: 10kb E2F1_top50 transfac_proM00939 17.8 0.412 E2F1 ** E2F1; E2F3; E2F4; TFDP1 (directAnnotation). TF_lowConf nEnrGenes rankAtMax 1: E2F5 (inferredBy_MotifSimilarity). 19 1144 2: E2F2; E2F5; E2F7; RB1 (inferredBy_MotifSimilarity). 21 2732 3: E2F1; E2F4; TFDP1; TFDP2 (inferredBy_MotifSimilarity). 24 3805 4: E2F2; E2F3; E2F4; E2F5; E2F7; E2F8; RB1; TFDP1 (inferredBy_MotifSimilarity). 20 1044 5: E2F2; E2F5; E2F7 (inferredBy_MotifSimilarity). 22 2253

Is there anything I can do to fix it? Thank you, Rentian

[wurentian]

By going through the code, I think my issue is because GENIE3 generated the linkList with redundant TF and Target links. Manually remove the redundant row by !duplicated() first before define row names seems working.

[s-aibar]

Thank you! This is now checked both in GENIE3 & the function to create the coexpression network