getTxDensity: getTxDensity Calculates transcript density.

In groHMM: GRO-seq Analysis Pipeline

Description

Calculates transcript density for transcripts which overlapps with annotations. For 'run genes together' or 'broken up a single annotation' errors, best overlapped transcripts or annotations are used.

Usage

getTxDensity(tx, annox, plot = TRUE, scale = 1000L, nSampling = 0L,
  samplingRatio = 0.1, ...)

Arguments

tx	GRanges of transcripts.
annox	GRanges of non-overlapping annotatoins.
plot	Logical. If TRUE, plot transcript density. Default: TRUE
scale	Numeric. Scaled size of a gene for transcript density calculation. Default: 1000L
nSampling	Numeric. Number of subsampling. Default: 0L
samplingRatio	Numeric. Ratio of sampling for annotations. Default: 0.1
...	Extra argument passed to mclapply.

Details

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors set the option 'mc.cores'.

Value

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

Author(s)

Minho Chae

Examples

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)

groHMM documentation built on Nov. 8, 2020, 8:09 p.m.