labelSeg: Helper functions for plotting
In epurdom/cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Description Usage Arguments Details Value Author(s) See Also Examples

Helper functions for plotting and working with chromosomes and segmentations

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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

hg19chromosomes,findOverlaps

data(mutData)
segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),
    end=c(1.8e7,max(mutData$position)),totalCpy=c(2,NA),
    markRegion=c(FALSE,TRUE))
if(require(GenomicRanges)) labelSeg(chr=segData$chromosome,
    start=segData$start,end=segData$end)
chr<-c("1","4","10","23","X")
chr[order(chr)]
chr[order(numChromosome(chr))]