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.
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.