gcapc (ChIP seq package) has peakcalling error
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dfinkels64 ▴ 10
@dfinkels64-14339
Last seen 4.2 years ago

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.

 

 

 

gcapc object error • 429 views
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