strandPileup: Strand specific read counts
In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

## S4 method for signature 'AlignedRead'
strandPileup(aligned, chrLen, extend,  coords=c("leftmost", "fiveprime"),
		compress = TRUE, plot = TRUE, ask = FALSE, ...)
## S4 method for signature 'data.frame'
strandPileup(aligned, chrLen, extend, coords=c("leftmost", "fiveprime"), 
		compress = TRUE, plot = TRUE, ask = FALSE, ...)

`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`.

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.

An object of class ReadCounts.

Peter Humburg

coverage, AlignedRead, callBindingSites

	## 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)