Question: quantsmooth chromosome sizes problem (genome release specification possible ?)
0
gravatar for bob.stephens.2005
5.2 years ago by
United States
bob.stephens.20050 wrote:

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

 

quantsmooth • 799 views
ADD COMMENTlink modified 5.2 years ago by Jan Oosting20 • written 5.2 years ago by bob.stephens.20050
Answer: quantsmooth chromosome sizes problem (genome release specification possible ?)
1
gravatar for Jan Oosting
5.2 years ago by
Jan Oosting20
Netherlands
Jan Oosting20 wrote:

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. 

ADD COMMENTlink written 5.2 years ago by Jan Oosting20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 182 users visited in the last hour