[Bioc-sig-seq] ChIPseqR question

[Hervé Pagès]

Hi Robert,

On 07/22/2010 09:19 AM, Robert Morris wrote:
>
> 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)

It looks like the "start", "end", "position" and/or "length" columns
of your data frame 'reads' contains NAs, which of course the
strandPileup() function doesn't like. If that's the case, you might
want to get rid of those rows that have NAs.

Cheers,
H.

PS: Please remember to provide your sessionInfo() and reproducible code
     when reporting problems like this one. See our Posting Guide:
       http://bioconductor.org/docs/postingGuide.html
     Thanks!

>
> 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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-- 
Hervé Pagès

Program in Computational Biology
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