windowAnalysis {groHMM} | R Documentation

## windowAnalysis Returns a vector of integers representing the counts of reads in a moving window.

### Description

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

### Usage

    windowAnalysis(reads, strand = "*", windowSize = stepSize,
      stepSize = windowSize, chrom = NULL, limitPCRDups = FALSE, ...)

### Arguments

`reads` | GenomicRanges object representing the position of reads mapping in the genome.
`strand` | Takes values of "+", "-", or "*". "*" denotes collapsing reads on both strands. Default: "*".
`windowSize` | Size of the moving window. Either windowSize or stepSize must be specified.
`stepSize` | The number of bp moved with each step.
`chrom` | Chromosome for which to return data. Default: returns all avaliable data.
`limitPCRDups` | Counts only one read mapping to each start site. NOTE: If set to TRUE, assumes that all reads are the same length (don't use for paired-end data). Default: FALSE.
`...` | Extra argument passed to mclapply

### Value

Returns a list object, each element of which represents a chromosome.

### Author(s)

Charles G. Danko and Minho Chae

### Examples

    S0mR1 <- as(readGAlignments(system.file("extdata", "S0mR1.bam",
         package="groHMM")), "GRanges")
    ## Not run:
    # Fp <- windowAnalysis(S0mR1, strand="+", windowSize=50)

[Package groHMM version 1.20.0 Index]