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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SwathXtend)
Loading required package: e1071
Loading required package: openxlsx
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SwathXtend/cleanLib.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cleanLib
> ### Title: Spectrum library cleanining
> ### Aliases: cleanLib
>
> ### ** 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)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.