decodeQuality: Conversion between numerical and ASCII representation of read...
In ChIPsim: Simulation of ChIP-seq experiments

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

These functions convert an ASCII encoded sequence of read qualities into a numeric vector of error probabilities and vice versa.

1 2	decodeQuality(quality, type = c("Illumina", "Sanger", "Solexa")) encodeQuality(quality, type = c("Illumina", "Sanger", "Solexa"))

`quality`	For `decodeQuality` a character string representing the read qualities for a single sequence read. For `encodeQuality` a numeric vector of error probabilities.
`type`	Type of encoding to use.

See extractQuality for a description of the currently supported encodings.

Either a numeric vector of error probabilities or a character string of encoded read quality scores. Each entry in the vector corresponds to one character in the input.

Peter Humburg

extractQuality

## decodeQuality and encodeQualty are the inverse operations 
## of each other as one might expect
quality <- "IIIIIIIIIIIIICIIGIIIIGII95III6II-II0"
errorProb <- decodeQuality(quality, type="Sanger")
qualitySanger <- encodeQuality(errorProb, type="Sanger")
all.equal(quality, qualitySanger)

## They can also be used to convert between encodings
qualityIllumina <- encodeQuality(errorProb, type="Illumina")