Using the quant smooth package to retrieve chromosome lengths produces this size for chromosome 18 (as example, others are also different): 76117153

however, both ensemble and ncbi give a value over 80 mbp for that chromosome. I used this command:

    chrlen<-lengthChromosome(chroms[i],"bases")
    print(paste("processing chrom ",chroms[i]," (",chrlen,")",sep=""))
    plot(c(0,chrlen),c(-2,nrow(lesions_list)+4.5),type="n",
         xaxt="n",yaxt="n",xlab="",ylab="",main=paste("Chromosome ",chroms[i],
         "(",peaks,")",sep=""))
    par(xpd=TRUE) #allow plotting outside margin
# draw chromosome at the bottom of plotting area...
    paintCytobands(chroms[i],units="bases",pos=c(1,2),width=1,legend=FALSE)

when I place hg19 based coordinates above the plot, the features extend beyond the end of the chromosome.

can we specify genome release version ? or supply our own bands files ?

thanks much !

Bob

I have updated the quantsmooth package for the new version of Bioconductor to address this issue. 

In the new version you can either use the annotation for the last few human genome versions or supply the data yourself.