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RcisTarget::addSignificantGenes error #37

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ysu2015 opened this issue Oct 19, 2023 · 0 comments
Open

RcisTarget::addSignificantGenes error #37

ysu2015 opened this issue Oct 19, 2023 · 0 comments

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@ysu2015
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ysu2015 commented Oct 19, 2023

Hi RcisTarget,

I got errors when running "RcisTarget::addSignificantGenes" by following the tutorial posted on "https://www.bioconductor.org/packages/release/bioc/vignettes/RcisTarget/inst/doc/RcisTarget_MainTutorial.html#Running_RcisTarget".
my script (and the results not the same as the tutorial):
txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
"hypoxiaGeneSet.txt", sep="/")
geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
head(geneLists$hypoxia)
motifRankings <- importRankings("mc_v10_clust/gene_based/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")

data(motifAnnotations_hgnc)
motifAnnotations_hgnc[199:202,]
(my results is the same as shown in the tutorial)

motif TF directAnnotation inferred_Orthology inferred_MotifSimil annotationSource  
bergman__tin NKX2-8 FALSE TRUE TRUE inferredBy_MotifSimilarity_n_Orthology  
bergman__tll DUX4 FALSE FALSE TRUE inferredBy_MotifSimilarity  
bergman__tll NR2E1 FALSE TRUE FALSE inferredBy_Orthology  
bergman__usp RXRA FALSE TRUE FALSE inferredBy_Orthology  
4 rows | 1-6 of 7 columns

###############################
motifs_AUC <- calcAUC(geneLists, motifRankings, nCores=1)
motifEnrichmentTable <- addMotifAnnotation(
motifs_AUC,
nesThreshold=3,
motifAnnot=motifAnnotations_hgnc,
highlightTFs=list(hypoxia=c("HIF1A", "EPAS1")))

class(motifEnrichmentTable)
[1] "data.table" "data.frame"

dim(motifEnrichmentTable)
[1] 24 8

head(motifEnrichmentTable[,-"TF_lowConf", with=FALSE]) (not the same as tutorial)

geneSet motif NES AUC highlightedTFs TFinDB TF_highConf
hypoxia 23459 4.13 0.0667 HIF1A, EPAS1    
hypoxia 19265 3.91 0.0643 HIF1A, EPAS1    
hypoxia 10830 3.58 0.0608 HIF1A, EPAS1    
hypoxia 10469 3.42 0.0591 HIF1A, EPAS1    
hypoxia 18527 3.41 0.0590 HIF1A, EPAS1    
hypoxia 19969 3.38 0.0586 HIF1A, EPAS1    
6 rows

follow the solution suggested by "jdenavascues" (Thanks a lot!!)
motifRankings@rankings <- dplyr::relocate(motifRankings@rankings, motifs)

and then it still did not go through.
motifEnrichmentTable_wGenes <- addSignificantGenes(motifEnrichmentTable,
geneSets=geneLists,
rankings=motifRankings,
nCores=1,
method="iCisTarget")

[1] 27090
Error in rccs[, sr] : subscript out of bounds

I have noticed that some users are having trouble with RcisTarget, especially regarding the different versions of the database.
Does anyone figure these out?

Y

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