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

Description Usage Arguments Methods Examples

Description

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

Usage

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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

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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.