windowAnalysis: windowAnalysis Returns a vector of integers representing the...

Description Usage Arguments Value Author(s) Examples

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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