combineTranscripts: combineTranscripts Combines transcripts.

In coregenomics/groHMM: GRO-seq Analysis Pipeline

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 each step in a plot. Default: FALSE

Value

Returns GRanges object of combined transcripts.

Author(s)

Minho Chae and Charles G. Danko

Examples

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

coregenomics/groHMM documentation built on May 7, 2019, 7:57 a.m.