breakTranscriptsOnGenes Breaks transcripts on genes

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Description

Breaks transcripts when they are overlapped with multiple well annotated genes.

Usage

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breakTranscriptsOnGenes(tx, annox, strand = "+", geneSize = 5000,
  threshold = 0.8, gap = 5, plot = FALSE)

Arguments

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

Value

Returns GRanges object of broken transcripts.

Author(s)

Minho Chae and Charles G. Danko

Examples

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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="+")

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