tag2bin: Convert the genome coordinates of aligned reads to bin-level...

In CSSP: ChIP-Seq Statistical Power

Description

Convert the genome coordinates of aligned reads to bin-level counts for all chromosomes.

Usage

tag2bin(tagdat, fragL = 200, binS = 200, prob = 1)

Arguments

tagdat	A list of the genome coordinates for starting positions of each read, with positive numbers representing the 5' strand and negative numbers representing the 3' strand. Each list component corresponds to a single chromosome.
fragL	A numeric value for the fragment length of reads. Default: 200.
binS	A numeric value for the bin-size for the bin-level counts to be constructed. Default: 200.
prob	A numeric value for the proportion of randomly sampled reads that will be used to create bin data. Default: 1 (use all reads).

Value

A list of the bin-level counts for each chromosome.

Author(s)

Chandler Zuo [e-mail]

Examples

data( tagdat_chip )
tag2bin( tagdat_chip, fragL = 100, binS = 100 )

CSSP documentation built on Nov. 8, 2020, 8:26 p.m.