Hello,
I am interested in using the ChIPseqR package to
predict nucleosome positions from MNase-seq data. I have loaded the
read positions, length and strand data into a data frame following the
package introduction pdf provided. However, when I try to construct the counts
object using the strandPileup function I get the following error:
> Chr1counts<-strandPileup(reads, chrLen=30427671, extend=1, plot=FALSE)
Error in solveUserSEW0(start = start, end = end, width = width) :
solving row 1: range cannot be determined from the supplied arguments (too
many NAs)
Error in coverage(IRanges(start = start1, width = extend), ...) :
error in evaluating the argument 'x' in selecting a method for function
'coverage'
Here is the traceback results:
> traceback()
4: coverage(IRanges(start = start1, width = extend), ...)
3: .local(aligned, chrLen, ...)
2: strandPileup(reads, chrLen = 30427671, extend = 1, plot = FALSE)
1: strandPileup(reads, chrLen = 30427671, extend = 1, plot = FALSE)
I would appreciate any insight into a solution for this problem.
Cheers,
Robert Morris
Robert Morris
Research Associate
Wyrick lab
Washington State University
Pullman, WA
USA
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