ChIPseqR (version 1.26.0)

strandPileup: Strand specific read counts

Description

Given a set of aligned reads this function computes the number of reads starting at each position in the genome.

Usage

"strandPileup"(aligned, chrLen, extend,  coords=c("leftmost", "fiveprime"),
		compress = TRUE, plot = TRUE, ask = FALSE, ...)
"strandPileup"(aligned, chrLen, extend, coords=c("leftmost", "fiveprime"), 
		compress = TRUE, plot = TRUE, ask = FALSE, ...)

Arguments

aligned

An object containing information about aligned reads (see Details).

chrLen

A numeric vector giving the length of each chromosome.

extend

A numeric value indicating how far reads should be extended.

coords

A character value indicating the coordinate system to use. See coverage for details.

compress

Logical indicating whether read counts should be compressed.

plot

If this is TRUE (the default) read coverage is plotted for all chromosomes.

ask

Logical. Setting this to TRUE causes the system to wait for user input before displaying a new plot. See devAskNewPage.

...

Further arguments to coverage.

Value

An object of class ReadCounts.

Details

The method for data.frame requires the column names to follow a strict naming scheme. Required columns are

‘chromosome’

A factor with chromosome names.

‘strand’

A factor with levels “-” and “+” indicating which strand the read mapped to.

‘start’ or ‘position’

Start position of read on chromosome.

‘end’ or ‘length’

End position of read or length of read respectively.

See Also

coverage, AlignedRead, callBindingSites

Examples

	## 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))))
	
	readPile <- strandPileup(reads, chrLen=500, extend=1, plot=FALSE)