cleanLib: Spectrum library cleanining
In SwathXtend: SWATH extended library generation and statistical data analysis

Description Usage Arguments Value Examples

Spectrum library cleanining

1 2	cleanLib(datLib, clean = TRUE, intensity.cutoff = 5, conf.cutoff = 0.99, nomod = FALSE, nomc = FALSE, enz = c("trypsin", "gluc", "chymotrypsin"))

`datLib`	a data frame for a spectrum library
`clean`	a logic value indicating if the library will be cleaned. Default value is TRUE.
`intensity.cutoff`	A number value to specify cut off for relative intensity of fragment ions. Only ions with intensity higher than the cut off value (default as 5) will be kept.
`conf.cutoff`	A number value to specify cut off for precursor confidence. Only ions with confidence higher than the cut off value (default as 0.99) will be kept.
`nomod`	a logic value, representing if the modified peptides and its fragment ions will be removed. True (default) means will be removed.
`nomc`	a logic value, representing if peptides with miss cleavages are removed. Default vaue is False (not to remove).
`enz`	A character string representing the enzyme which can be one of "trypsin" (defalut), "gluc", or "chymotrypsin"

a data frame of a cleaned spectrum library by the specified criteria

file <- paste(system.file("files",package="SwathXtend"),"Lib1.txt",sep="/")
dat <- read.delim2(file,sep="\t",header=TRUE,stringsAsFactors=FALSE)
dat <- canonicalFormat(dat)
dat <- cleanLib(dat)