ReadCounts: Class "ReadCounts"

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

Description

Represents counts of (possibly extended) reads for each strand of the genome.

Usage

ReadCounts(counts=list(), names=NULL, compress=TRUE)

Arguments

counts	A list of read counts. Each component is a two column matrix of strand specific read counts for a chromosome.
names	Character vector of chromosome names. If this is NULL the names of counts are used instead.
compress	Logical indicating whether read counts should be compressed.

Objects from the Class

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

Slots

counts:

Object of class "list" with one component per chromosome, containing a matrix of read counts (one column per strand).

Methods

[<-

signature(x = "ReadCounts", i = "ANY", j = "missing"): Replace read counts for chromosomes indicated by i.

[

signature(x = "ReadCounts", i = "ANY", j = "missing", drop = "missing"): Returns list of read counts for chromosomes indicated by i.

[[<-

signature(x = "ReadCounts", i = "ANY", j = "missing"): Replace read counts for chromosome i.

[[

signature(x = "ReadCounts", i = "ANY", j = "missing"): Returns read counts for chromosome i.

$<-

signature(x = "ReadCounts"): Replace read counts for chromosome i (by name).

$

signature(x = "ReadCounts"): Returns read counts for chromosome i (by name).

callBindingSites

signature(data = "ReadCounts"): Predict bindingsites from read counts.

chrLength

signature(x = "ReadCounts", subset = "ANY"): Returns length of all chromosomes represented in x.

lapply

signature(X = "ReadCounts"): Apply function to read counts for each chromosome.

length<-

signature(x = "ReadCounts"): Change the number of chromosomes represented by x to value.

length

signature(x = "ReadCounts"): Number of chromosomes represented by x.

names<-

signature(x = "ReadCounts", value = "ANY"): Change names of chromosomes.

names

signature(x = "ReadCounts"): Chromosome names.

nreads

signature(x = "ReadCounts", byStrand = "Logical", subset = "ANY"): Returns the number of reads on each chromosome, split by strand (if byStrand is TRUE).

sapply

signature(X = "ReadCounts"): Apply function to read counts for each chromosome.

Author(s)

Peter Humburg

See Also

BindScore, strandPileup , compress, decompress

Examples

showClass("ReadCounts")

## 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=FALSE)

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

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