Hi all, I am currently using online data set just to run RAPIDR analysis. I have Chromosome 1.bam file for 2 samples. library(RAPIDR) library(SummarizedExperiment) makeBinnedCountsFile(bam.file.list=c("file1_chr1.bam", "file2_chr1.bam"), sampleIDs=c("sample1", "sample2"), 'output.fname', k=20000) after runnning this i am getting warning
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Then i treid next step that is running refset
data(outcomes)
data(gcContent)
T21.pos <- which(outcomes$Dx == "T21")
chr.lens <- sapply(gcContent, length)
chr.names <- names(chr.lens)
header <- c("SampleID")
for (i in 1:length(chr.lens))
{
header <- c(header, rep(chr.names[i], chr.lens[i]))
}
nbins <- sum(chr.lens)
ncols <- nbins + 1
binned.counts <- matrix(nrow = nrow(outcomes), ncol = ncols)
for (i in 1:nrow(binned.counts)) {
binned.counts[i,] <- rpois(ncols, lambda = 100)
if (i %in% T21.pos) {
binned.counts[i, 139087:141493] <- rpois(chr.lens[21], lambda = 115)
}
}
binned.counts[,1] <- outcomes$SampleID
colnames(binned.counts) <- header
Again with this i am getting the error
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
Then i alone rerun the createReferenceSet
ref.set <- createReferenceSetFromCounts(output.fname, outcomes, gcCorrect = FALSE, PCA = FALSE, method = "NCV")
Again i got error
Loading binned counts file
Error in fread(binned.counts.file, sep = ",", colClasses = list(character = 1), :
object 'output.fname' not found
though i have made output.fname still it is giving me this error
I am not able to tackle please help.
Please note that RAPIDR is a CRAN package and is not on Bioconductor. You might best ask the maintainer of that package directly as we can not guarantee the maintainer is subscribed to this mailing list.