Dear developer & users,
Hi, I've been trying GreyListChIP but was not succeed when using own bam file (The package installation is alright, which tested by the sample data)
Here's the code:
library(GreyListChIP) library(BSgenome.Mmusculus.UCSC.mm10) path <- system.file("extra", package="GreyListChIP") fn <- file.path(path,"T1-D0-I.dup.removed.sort.bam") gl <- new("GreyList",BSgenome.Mmusculus.UCSC.mm10) gl <- countReads(gl,fn) gl <- calcThreshold(gl,reps=100,sampleSize=30000,p=0.99,cores=4)
Warning generated by countReads:
In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.)
Warning generated by calcThreshold:
Error in stuff[[x]] : subscript out of bounds
when I inspect the gl, only the tiles and file path return. I think the I was stuck since the countReads step.
GreyList on Mus musculus (UCSC mm10) tiles: 5333798 files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/GreyListChIP/extra/T1-D0-I.dup.removed.sort.bam
Any help will be appreciated. Thanks a lot!