runMetaGene {groHMM} | R Documentation

## Runs metagene analysis for sense and antisense direction.

### Description

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

### Usage

    runMetaGene(features, reads, anchorType = "TSS", size = 100L,
      normCounts = 1L, up = 10000L, down = NULL, sampling = FALSE,
      nSampling = 1000L, samplingRatio = 0.1, ...)

### Arguments

`features` | GRanges A GRanges object representing a set of genomic coordinates, i.e., set of genes.
`reads` | GRanges of reads.
`anchorType` | Either 'TSS' or 'TTS'. Metagene will be centered on the transcription start site(TSS) or transcription termination site(TTS). Default: TSS.
`size` | Numeric. The size of the moving window. Default: 100L
`normCounts` | Numeric. Normalization vector such as average reads. Default: 1L
`up` | Numeric. Distance upstream of each feature to align and histogram. Default: 1 kb
`down` | Numeric. Distance downstream of each feature to align and histogram. If NULL, down is same as up. Default: NULL
`sampling` | Logical. If TRUE, subsampling of Metagene is used. Default: FALSE
`nSampling` | Numeric. Number of subsampling. Default: 1000L
`samplingRatio` | Numeric. Ratio of sampling for features. Default: 0.1
`...` | Extra argument passed to mclapply.

### Value

A list of integer-Rle for sense and antisene.

### Author(s)

Minho Chae

### Examples

    features <- GRanges("chr7", IRanges(start=1000:1001, width=rep(1,2)),
     strand=c("+", "-"))
    reads <- GRanges("chr7", IRanges(start=c(1000:1003, 1100:1101),
     width=rep(1, 6)), strand=rep(c("+","-"), 3))
    ## Not run:
    # mg <- runMetaGene(features, reads, size=4, up=10)

[Package groHMM version 1.14.0 Index]