Nothing
#R
# $HeadURL: http://fgcz-svn.unizh.ch/repos/fgcz/testing/proteomics/R/protViz/R/parentIonMass.R $
# $Id: parentIonMass.R 6178 2014-02-27 09:33:30Z cpanse $
# $Date: 2014-02-27 10:33:30 +0100 (Thu, 27 Feb 2014) $
#fetuinPeptides<-c('LCPGR', 'GSVIQK', 'QYGFCK', 'AHYDLR', 'EVVDPTK', 'CNLLAEK', 'ALGGEDVR', 'HTLNQIDSVK', 'QDGQFSVLFTK', 'CDSSPDSAEDVR', 'TPIVGQPSIPGGPVR', 'LCPDCPLLAPLNDSR', 'QQTQHAVEGDCDIHVLK', 'HTFSGVASVESSSGEAFHVGK', 'EPACDDPDTEQAALAAVDYINK', 'AQFVPLPVSVSVEFAVAATDCIAK', 'SFVLLFCLAQLWGCHSIPLDPVAGYK', 'VVHAVEVALATFNAESNGSYLQLVEISR', 'RPTGEVYDIEIDTLETTCHVLDPTPLANCSVR', 'VTCTLFQTQPVIPQPQPDGAEAEAPSAVPDAAGPTPSAAGPPVASVVVGPSVVAVPLPLHR')
parentIonMass <- function(sequence, fixmod=NULL, NTerm=1.007825) {
if (!is.character(sequence)) {
stop ("argument x must be a character")
}else if (length(fixmod)>0 & length(fixmod)!=26){
stop ("length of fixmod must be 26. One value for each letter from 1 to 26.")
}else if (length(fixmod)==26){
out <- .C("computeParentIonMass2",
n=as.integer(length(sequence)),
pepSeq=as.character(sequence),
pim=as.double(rep(0,length(sequence))),
M_=as.double(fixmod),
M_term_=as.double(NTerm)
)
}else{
out <- .C("computeParentIonMass",
n=as.integer(length(sequence)),
pepSeq=as.character(sequence),
pim=as.double(rep(0,length(sequence)))
)
}
return(out$pim)
}
# Christian Trachsel
# Christian Panse <cp@fgcz.ethz.ch>
# 2013-03-22 1mass.min
# takes as input a vector of peptide sequences and computes
# 2+,3+,4+ mass histograms
.gasPhaseFragQuantiles<-function(peptides, mass.min=300, mass.max=1250, fixmod=NULL, NTerm=1.007825){
pim <- parentIonMass(peptides, fixmod, NTerm)
pim2 <- (pim + 1.00782)/2
pim3 <- (pim + 2*1.00782)/3
pim4 <- (pim + 3*1.00782)/4
# breaks for Histogram
bb<-seq(0,max(pim), by=10);
hist(pim2, bb, xlim=c(mass.min,mass.max), prob=FALSE, xlab='mass bin size 10 Dalton')
hist(pim3, bb, xlim=c(mass.min,mass.max), prob=FALSE, xlab='mass bin size 10 Dalton')
hist(pim4, bb, xlim=c(mass.min,mass.max), prob=FALSE, xlab='mass bin size 10 Dalton')
hist(c(pim2, pim3, pim4), bb, xlim=c(mass.min,mass.max), prob=FALSE)
ss<-(sort(c(pim2, pim3, pim4)))
sss<-ss[mass.min < ss & ss < mass.max]
q <- quantile(sss)
hist(sss, breaks=q, prob=FALSE, xlab="mass")
axis(3, q, round(q))
# not covert % by mass range
100 * (length(ss[ ! ((mass.min < pim2 & pim2 < mass.max)
| (mass.min < pim3 & pim3 < mass.max)
| (mass.min < pim4 & pim4 < mass.max)) ]) / length(peptides))
}
# s<-read.table("p1239_sequences.txt")
# pdf("p1239-pep-charge-mass-hist.pdf", 19,12)
# par(mfrow=c(2,3),mar=c(6,4,6,1));
# gasPhaseFragQuantiles(as.character(s$V1))
# dev.off()
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