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

In coregenomics/groHMM: GRO-seq Analysis Pipeline

Description

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

Usage

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

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 available data.

Value

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

Author(s)

Charles G. Danko and Minho Chae

Examples

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

coregenomics/groHMM documentation built on May 7, 2019, 7:57 a.m.