breakTranscriptsOnGenes {groHMM} | R Documentation |
Breaks transcripts when they are overlapped with multiple well annotated genes.
breakTranscriptsOnGenes(tx, annox, strand = "+", geneSize = 5000, threshold = 0.8, gap = 5, plot = FALSE)
tx |
GRanges of transcripts. |
annox |
GRanges of non-overlapping annotations for reference. |
strand |
Takes "+" or "-" Default: "+" |
geneSize |
Numeric. Minimum gene size in annox to be used as reference. Default: 5000 |
threshold |
Numeric. Ratio of overlapped region relative to a gene width. Transcripts only greater than this threshold are subjected to be broken. Default: 0.8 |
gap |
Numeric. Gap (bp) between broken transcripts. Default: 5 |
plot |
Logical. If set to TRUE, show each step in a plot. Default: FALSE |
Returns GRanges object of broken transcripts.
Minho Chae and Charles G. Danko
tx <- GRanges("chr7", IRanges(1000, 30000), strand="+") annox <- GRanges("chr7", IRanges(start=c(1000, 20000), width=c(10000,10000)), strand="+") bPlus <- breakTranscriptsOnGenes(tx, annox, strand="+")