peakcount.chr: Compute the number of aligned reads overlapping peaks for one...

Description Usage Arguments Value Author(s) Examples

View source: R/process_bin.R

Description

Compute the number of aligned reads overlapping peaks for one chromosome.

Usage

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peakcount.chr(tagdat, peakpos, fragL = 200, unique = FALSE)

Arguments

tagdat

A numeric vector of the genome coordinates for the starting positions of aligned reads. The signs of coordinates represent their strand direction, with positive numbers representing the 5' strand and negative numbers representing the 3' strand.

peakpos

A 2-column matrix matrix containing the left and right position of the peaks for one chromosome.

fragL

A numeric value for the fragment length of the sequencing reads. Default: 200.

unique

A logical value for whether only reads mapping to unique nucleotide positions are counted.

Value

A numeric vector of the number of overlapping tags for all peaks.

Author(s)

Chandler Zuo zuo@stat.wisc.edu

Examples

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

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