findPeaks: find peaks.

Description Usage Arguments Value Examples

Description

find peaks.

Usage

1
2
3
findPeaks(files, chr = 1:19, fraglen = 200, rlen = 100, min_win = 1,
  max_win = 100, blocksize = 10000, zthresh = 5, min_count = 0.1,
  grid = NA, filetype = "bam", save = FALSE)

Arguments

files

Character vector containing paths of files to be analyzed.

chr

Integer specifying which chromosme to limit analysis to.

fraglen

Integer indicating the average DNA fragment length in bp

rlen

Integer indicating the read length in bp

min_win

Integer indicating the minimum window size to be used in constructing grid

max_win

Integer indicating the maximum window size to be used in constructing grid

blocksize

Integer indicating how large of a chunk of the chromosome will be analyzed at a time

zthresh

Z-score threshold over which peaks will be retained.

min_count

Double indicating a small amount to use as minimum count instead of zero.

grid

Numeric vector grid

filetype

Character, either "bam" or "bed"

save

Boolean, save files.

Value

s.

Examples

1
2
3
bam <- system.file("extdata", "test.bam", package = "DEScan")
peaks <- findPeaks(bam, chr = 1, filetype = "bam")
head(peaks)

jnkoberstein/DEScan documentation built on May 29, 2019, 11:39 a.m.