RAPIDR analysis Pipeline
0
0
Entering edit mode
@rayagirish-9685
Last seen 6.2 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 • 865 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 811 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6