R/data.R

In eahrne/SafeQuant: A Toolbox for the Analysis of Proteomics Data

#'   Kinase motifs
#'
#'  Human Protein Reference Database Serine/Threonine motifs
#'  http://www.hprd.org/serine_motifs
#'  The variables are as follows:
#'
#' @format A data frame with 175 rows and 2 variables:
#' \describe{
#'   \item{motif}{kinase motif)}
#'   \item{kinase}{kinase}
#' }
"kinaseMotif"

if(F){
	 library(magrittr)
	 
	  #kinaseMotif =  read.csv(file="~/dev/R/workspace/CristinaPhospho/data/motifsEtc/HPRD_kinas_motifs.csv")
	  kinaseMotif =  read.csv(file="~/dev/R/workspace/CristinaPhospho/data/motifsEtc/HPRD_kinas_motifs_curated.csv",sep="\t")
	  names(kinaseMotif) = c("motif","kinase","binding")
	  # discard double phoshpho e.g. pS*PXX[pS/pT]
	  selDoubleS = lapply(kinaseMotif$motif,  function(t){  gregexpr("pS",t)} %>%  unlist %>% length   ) %>% unlist %>% as.vector > 1
	  selDoubleT = lapply(kinaseMotif$motif,  function(t){  gregexpr("pT",t)} %>%  unlist %>% length   ) %>% unlist %>% as.vector > 1
	  kinaseMotif = kinaseMotif[!(selDoubleS | selDoubleT | grepl("\\*",kinaseMotif$motif) ),]
	  kinaseMotif$regExpr = kinaseMotif$motif %>% gsub(("X"),".",.) %>% gsub("(p)([STY])","(p\\2)",.) %>%  gsub("\\)\\/\\(",")|(",.) %>%  gsub("\\[\\(","((",.)  %>%  gsub("\\)\\]","))",.) %>% gsub("\\/","",.)
	  kinaseMotif$kinase = gsub("Kinase","kinase",kinaseMotif$kinase)
	  kinaseMotif = unique(kinaseMotif)
	  save(kinaseMotif, file="~/dev/R/workspace/SafeQuant/data/kinaseMotif.rda")
	 # grepl("(pS)|(pT)","XXXpSXXX", ignore.case = FALSE)
	 # grepl("KKKKKK((pS)|(pT)).","KKKKKKpTX")
	 # grepl("R.R..((pS)|(pT))[FL]","RXRXXpSL")
	 # grepl("R.R..((pS)|(pT))[FL]X","RXRXXpSL")
	 # grepl("R.R..((pS)|(pT))[FL]","RXRXXpTLX")
	 # grepl("...","KK")
	 
	 #lapply(kinaseMotif$regExpr,function(t){grepl(t,"AAA")})
	#kinaseMotif[kinaseMotif$regExpr == '[ED(pT)|(pY)).(pY)EE',] 
	
}