RAPIDR analysis Pipeline
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@rayagirish-9685
Last seen 3.8 years ago

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.

 

 

Rapidr • 452 views
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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.

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