countHitsWindow: Compute number of hits in a moving window along the...

In htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data

Description

Computes a smoothed number of hits along the chromosome by using moving windows of user specified size.

Usage

countHitsWindow(x, chrLength, windowSize = 10^4 - 1)

Arguments

x	Object containing hits (start, end and chromosome). Currently only RangedData objects are accepted.
chrLength	Named vector indicating the length of each chromosome in base pairs.
windowSize	Size of the window used to smooth the hit count.

Methods

signature(x = "RangedData")

x contains chromosome, start and end positions for each hit.

Examples

set.seed(1)
st <- round(rnorm(1000,500,100))
st[st>=10000] <- 10000
strand <- rep(c('+','-'),each=500)
space <- rep('chr1',length(st))
x <- RangedData(IRanges(st,st+38),strand=strand,space=space)
countHitsWindow(x, chrLength=c(chr1=10000), windowSize=99)

htSeqTools documentation built on May 6, 2019, 3:39 a.m.