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

In groHMM: GRO-seq Analysis Pipeline

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)

groHMM documentation built on Nov. 8, 2020, 8:09 p.m.