groHMM (version 1.6.0)

getTxDensity: getTxDensity Calculates transcript density.

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.

Value

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

Details

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

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)