/
coverage.R
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/
coverage.R
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######################################################################################
#################################################################
######## script to compute proteome coverage given cleavage
######## output from cut.predict
coverage=function(object=Spombe){
#### how many proteases were used?
cleaved.l<-length(object@cleaved)
###loop over the cleaved.l
for(j in 1:cleaved.l){
peps2<-unlist(object@cleaved[j])
totalvec<-c(rep(0,sum(nchar(peps2))))
peplengths<-nchar(peps2)
pepvec.l<-length(peplengths)
start<-1
end<-peplengths[1]
if(peplengths[1]>=7&peplengths[1]<=35){
totalvec[start:end]<-rep(1,times=peplengths[1])
}
start<-end+1
for(i in 2:pepvec.l){
end<-peplengths[i]+end
if(peplengths[i]>=7&&peplengths[i]<=35){
totalvec[start:end]<-rep(1,times=peplengths[i])
}
start<-start+peplengths[i]
print(i)
}
### this part puts the binary outcome into object@coverage
if(j==1){object@coveragevec<-totalvec}
if(j>=2){object@coveragevec<-object@coveragevec+totalvec}
}
notcovered<-length(totalvec[totalvec==0])
total<-length(totalvec)
pctnotcovered<-notcovered/total
pctcovered<-1-pctnotcovered
object@coverage<-c(covered=pctcovered,not=pctnotcovered)
pie(object@coverage,main="predicted coverage")
return(object)
}