readError: Introduce errors into read sequence based on quality scores
In ChIPsim: Simulation of ChIP-seq experiments

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

Given a read sequence and quality this function introduces errors by first choosing positions that should be modified based on the quality score and then exchanges nucleotides based on the probabilities given in prob.

1 2	readError(read, qual, alphabet = c("A", "C", "G", "T"), prob = defaultErrorProb(), ...)

`read`	A character string representing a read sequence.
`qual`	Numeric vector of read error probabilities.
`alphabet`	Alphabet used for read sequence.
`prob`	Nucleotide exchange probabilities.
`...`	Further arguments (currently ignored).

If the read sequence contains letters that are not part of alphabet they are replaced by the first entry of alphabet before positions of sequencing errors are determined. The alphabet used has to match the names used in prob.

The modified read sequence.

Peter Humburg

defaultErrorProb, readSequence

set.seed(42)

## generate sequence read and quality
quality <- paste(sample(unlist(strsplit(rawToChar(as.raw(33:126)),"")), 
	36, replace = TRUE), collapse="")
errorProb <- decodeQuality(quality, type = "Sanger")
read <- paste(sample(c("A", "C", "G", "T"), 36, replace = TRUE), 
	collapse = "")

## use readError to introduce sequencing errors
read2 <- readError(read, errorProb)

all.equal(read, read2)  ## "1 string mismatch"