Description Usage Arguments Details Value Author(s) See Also Examples
Helper functions for plotting and working with chromosomes and segmentations
1 2 3 | labelSeg(chr, start, end, pctOv = 0.1)
numChromosome(chr)
divideGenome(size=10)
|
chr |
chromosome |
start |
start position of segment |
end |
end position of segment |
pctOv |
required amount of percent overlap needed in order to report |
size |
Size, in MB, of the desired equally spaced divisions of the genome |
labelSeg creates labels ‘p’, ‘q’, and ‘pq’ for segmentations based on the overlap of the segment with the p/q portions of the human chromosome (hg19). It uses the data stored in hg19chromosomes with the package (under the directory 'extdata', not as a dataset of the package). Uses the findOverlaps function of GenomicRanges.
numChromosome takes character valued chromosome labels (“1”,“2”,...,“X”,“Y”) and converts them into values 1:23. This is useful for sorting chromosome values, for example.
divideGenome makes segments of the genome of size equal to 'size' times 1e6, i.e. size-MB length intervals, also based on the hg19chromosomes data described above.
vector of numerical values between 1:23
Elizabeth Purdom
1 2 3 4 5 6 7 8 9 | data(mutData)
segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),
end=c(1.8e7,max(mutData$position)),totalCpy=c(2,NA),
markRegion=c(FALSE,TRUE))
if(require(GenomicRanges) & require(IRanges)) labelSeg(chr=segData$chromosome,
start=segData$start,end=segData$end)
chr<-c("1","4","10","23","X")
chr[order(chr)]
chr[order(numChromosome(chr))]
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.