getTxDensity: getTxDensity Calculates transcript density.

In omsai/groHMM: GRO-seq Analysis Pipeline

Description

Calculates transcript density for transcripts which overlaps with annotations. For 'combined' or 'broken up' errors, best overlapped transcripts or annotations are used.

Usage

getTxDensity(tx, annox, plot = FALSE, scale = 1000L, BPPARAM = bpparam())

Arguments

tx	GRanges of transcripts.
annox	GRanges of non-overlapping annotations.
plot	Logical. If TRUE, plot transcript density. Default: FALSE
scale	Numeric. Scaled size of a gene for transcript density calculation. Default: 1000L
BPPARAM	Registered backend for BiocParallel. Default: BiocParallel::bpparam()

Value

Returns a list of FTD, TTD, PostTTS, and TUA.

Author(s)

Minho Chae

Examples

library(GenomicRanges)
tx <- GRanges("chr7", IRanges(start=seq(1000,4000, by=1000),
width=seq(1000, 1300, by=100)), strand=rep("+", 4))
annox <- GRanges("chr7", IRanges(start=seq(1100,4100, by=1000),
width=seq(900, 1200, by=100)), strand=rep("+", 4))
## Not run:
# density <- getTxDensity(tx, annox)

omsai/groHMM documentation built on May 24, 2019, 2:18 p.m.