groHMM (version 1.6.0)

combineTranscripts: combineTranscripts Combines transnscipts.

Description

Combines transcripts that are within the same gene annotation, combining smaller transcripts for genes with low regulation into a single transcript representing the gene.

Usage

combineTranscripts(tx, annox, geneSize = 1000, threshold = 0.8, plot = FALSE)

Arguments

tx

GRanges of transcripts.

annox

GRanges of non-overlapping annotations for reference.

geneSize

Numeric. Minimum gene size in annotations to be used as reference. Default: 1000

threshold

Numeric. Ratio of overlapped region relative to transcript width. Transcripts only greater than this threshold are subjected to be combined. Default: 0.8

plot

Logical. If set to TRUE, show easch step in a plot. Default: FALSE

Value

Returns GRanges object of combined transcripts.

Examples

tx <- GRanges("chr7", IRanges(start=c(1000, 20000), width=c(10000,10000)),
strand="+")
annox <- GRanges("chr7", IRanges(1000, 30000), strand="+")
combined <- combineTranscripts(tx, annox)