createBins: Partitions a genome into bins of a fixed length and counts...

In welch16/ChIPUtils: ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures

Description

Partitions a chromosome into fixed length bins and counts the number of extended fragments that overlap each bin

Usage

createBins(binSize, chipdata = NULL, chrom = NULL, fragLen = 1)

Arguments

binSize	A integer value used to partition the chromosome
chipdata	A ChIPdata object
chrom	A GRanges object specifying the genome to bin. The maximum length used to create the bins is gonna be used the integer part of (chromLen / fragLen) times fragLen for each chromosome.
fragLen	An integer value used to extend the fragments. The default value is one, to count only the 5' ends that overlaps the bins. For PE reads is going to be ignored

Value

A GRanges object. If a reads object is present then is going to count the number of extended fragments per bin

welch16/ChIPUtils documentation built on May 4, 2019, 4:18 a.m.