findPeaks: find peaks.

In jnkoberstein/DEScan: Differential Enrichment Scan

Description

find peaks.

Usage

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

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.