getTxDensity {groHMM} | R Documentation

## 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.

### 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)

[Package groHMM version 1.18.0 Index]