Question: Error while running ExomeDepth
0
gravatar for ashwani.vit
3.7 years ago by
United States
ashwani.vit0 wrote:

Hello,

While running exomeDepth, I got the following error: Error in [<-.data.frame(*tmp*, , column.name, value = c(NA_character_, : replacement has 2 rows, data has 0 Calls: AnnotateExtra -> AnnotateExtra -> [<- -> [<-.data.frame

I have 2 control samples and 2 test samples. Please help out!

Regards, Ashwani

R wgs • 1.0k views
ADD COMMENTlink written 3.7 years ago by ashwani.vit0

Could you post all code up to the point the error was produced?

ADD REPLYlink written 3.7 years ago by WouterDeCoster43k

for (i in 1:nsamples){ my.choice <- select.reference.set (test.counts = ExomeCount.mat[,i], reference.counts = my.reference.set, bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000, n.bins.reduced = 10000) my.matrix <- as.matrix(ExomeCount.dafr[, my.choice$reference.choice,drop=FALSE]) my.reference.selected <- apply(X=my.matrix,MAR = 1,FUN = sum)

all.exons <- new('ExomeDepth', test = ExomeCount.mat[,i], reference = my.reference.selected, formula = 'cbind(test, reference) ~ 1')

all.exons <- CallCNVs(x = all.exons, transition.probability = 10^-4, chromosome = ExomeCount.dafr$space, start = ExomeCount.dafr$start, end = ExomeCount.dafr$end, name = ExomeCount.dafr$names) #head(all.exons@CNV.calls) #head(all.exons@CNV.calls[order (all.exons@CNV.calls$BF,decreasing=TRUE),])

exons.hg19.X.GRanges <- GRanges(seqnames = exons.hg19.X$chromosome, IRanges(start=exons.hg19.X$start,end=exons.hg19.X$end), names = exons.hg19.X$name) all.exons <- AnnotateExtra(x = all.exons, reference.annotation = exons.hg19.X.GRanges, min.overlap = 0.0001, column.name = 'exons.hg19.X')

}

The error is thrown at the annotation stage. I am using exons,hg19.X.

ADD REPLYlink written 3.7 years ago by ashwani.vit0
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