SwathXtend (version 1.0.0)

cleanLib: Spectrum library cleanining

Description

Spectrum library cleanining

Usage

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

Arguments

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"

Value

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

Examples

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)