RLEReadCounts-class: Run-length Encoded Read Counts

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description

This class provides a memory efficient representation of strand specific read counts.

Objects from the Class

Objects can be created by calls of the form ReadCounts(counts, names, compress = TRUE) or by calls to strandPileup.

Slots

counts:

Object of class "list" with one component per chromosome, containing a read counts encoded in an object of class RleList.

Extends

Class "ReadCounts", directly.

Methods

chrLength

signature(x = "RLEReadCounts"): Returns length of all chromosomes represented in x.

decompress

signature(x = "RLEReadCounts"): Expands read counts and returns object of class ReadCounts.

nreads

signature(x = "RLEReadCounts"): Returns the number of reads on each chromosome, split by strand (if byStrand is TRUE)

plot

signature(x = "RLEReadCounts", y = "missing"): Generates plots of read counts.

Author(s)

Peter Humburg

See Also

ReadCounts, RleList

Examples

showClass("RLEReadCounts")

## generate some very simple artificial read data
set.seed(1)
fwd <- sample(c(50:70, 250:270), 30, replace=TRUE)
rev <- sample(c(197:217, 347:417), 30, replace=TRUE)
## create data.frame with read positions as input to strandPileup
reads <- data.frame(chromosome="chr1", position=c(fwd, rev), 
	length=25, strand=factor(rep(c("+", "-"), times=c(30, 30))))

## create object of class ReadCounts
readPile <- strandPileup(reads, chrLen=500, extend=1, plot=FALSE, compress=TRUE)

names(readPile)
length(readPile)
sapply(readPile, sum)

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.