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Question: gcapc (ChIP seq package) has peakcalling error
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gravatar for dfinkels64
11 days ago by
dfinkels640
dfinkels640 wrote:

HI Anyone,

I've been trying to run my own bam file through this program (gcapc) with  limited success.  After correcting the bam header and  stripping it down to a single chromosome (chr1 hg19) to meet memory requirements. I was able to get all the way through error free to the peak calling step,  after defining cov and gcb and bdw.  I'm running 3.4 in a Linux cluster xterm using 20G (this fixed the memory problem as on my desktop gcapc tried to create a 3.6 G vector).  At this point I'm very close to giving up on this package.    I'm hoping someone can help.

 

library(gcapc)
bf<-("/research/rgs01/project_space/pottsgrp/MAGE/cmpb/SJ12_chr.bam")
 cov <- read5endCoverage(bf)
 bdw <- bindWidth(cov, range=c(50L,300L), step=10L)
 gcb <- gcEffects(cov, bdw, sampling=c(0.25,1), plot=FALSE, model='poisson')
 peaks <- gcapcPeaks(cov, gcb, bdw, plot=FALSE, permute=100L)

All the 100 permutations ran (see below)

......... permutation 100
...... reporting peaks
Error in validObject(.Object) :
  invalid class “NativeNSBS” object: invalid object for slot "upper_bound" in class "NativeNSBS": got class "numeric", should be or extend class "integer"
In addition: Warning message:
In NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,  :
  NAs introduced by coercion to integer range

From what I can tell this is vector storage object in R I'm unfamiliar with, so I don't know how to fix it.

 

 

 

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