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

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Description

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

Usage

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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

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

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