HI,
directory<- "/home/arunksa111/NewData"
GetFileList <- function(directory,number){
setwd(directory)
filelist1<-dir()[file.info(dir())$isdir]
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
direct<-lapply(direct,function(x) paste(directory,"/",x,sep=""))
lista<-unlist(direct)
output<- list(filelist1,lista)
return(output)
}
file.list.names<-GetFileList(directory,23) [[1]]
lista<-GetFileList(directory,23) [[2]]
FacGroup<-c(0,1,1,1,0,2,2,2)
ReadDir<-function(FacGroup){
list.new<-lista[FacGroup!=0]
read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t",stringsAsFactors=FALSE))
names(read.list)<-file.list.names[FacGroup!=0]
return (read.list)
}
ListFacGroup<-ReadDir(FacGroup)
ListFacGroupSub<-lapply(ListFacGroup,head)
Pro<- function(lista,FDR_k) {
split.list<- split(lista,names(lista))
seq.mod.z<- lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x) x[x[["FDR"]]<
FDR_k,c("Seq","Mod","z","Pro")]))
names(seq.mod.z)<- names(split.list)
folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
library(plyr)
library(data.table)
merge.data<-lapply(folder.name,function(x) lapply(x,function(x1) {x1<-
data.table(x1);x1[,Pro:=paste(Pro,collapse=","),by=c("Seq","Mod","z")]}))
count.Pro<-lapply(merge.data,function(x) lapply(x,function(x1) {
x1$counts<-sapply(x1$Pro,function(x2)
length(gsub("\\s","",unlist(strsplit(x2,",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.ProUnique<-lapply(count.Pro,function(x) lapply(x,unique))
#count Pro by group (2-columns)
Pro.group<-lapply(count.ProUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
#Pro.group1<-Pro.group[lapply(Pro.group,length)!=0]
res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),Pro.group)
res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
res
}
Pro(ListFacGroupSub,0.05)
# Seq Mod z c2 c3 c4 t2 t3 t4
#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2 0 0 1 1 0 1
#2 aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2 0 0 1 1 0 1
#3 aAAAAAAAAAGAAGGR 1-n_acPro/ 2 2 0 2 2 2 2
#4 aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2 0 0 2 0 0 2
#5 AAAAAAAkAAK 8-K_ac/ 2 1 0 0 0 0 0
#6 AAAAAAALQAK 2 0 2 0 2 0 0
#7 aAAAAAGAGPEMVR 1-n_acPro/ 2 2 2 2 2 2 2
#8 aAAAAATAAAAASIR 1-n_acPro/ 2 0 0 0 0 1 0
#9 aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2 0 0 0 18 0 0
#10 aAAAAEQQQFYLLLGNLLSPDNVVR 1-n_acPro/ 2 18 0 0 0 0 0
#11 aAAAAEQQQFYLLLGNLLSPDNVVR 1-n_acPro/ 3 0 18 0 0 0 0
#12 aAAAAVGNAVPCGAR 1-n_acPro/ 2 0 1 0 0 0 0
ProCt<-Pro(ListFacGroup,0.05)
dim(ProCt)
#[1] 29429 9
A.K.
________________________________
From: Vera Costa <veracosta...@gmail.com>
To: arun <smartpink...@yahoo.com>
Sent: Thursday, May 16, 2013 1:37 PM
Subject: Re: question
Hi.
Other thing that I need (and I sent a new format data) is to count data like
function spec, but for the variable "pro". The idea is exactly the same, but
I'm with some dificulties because the format of the data... The Pro is like
">sp|Q86U42|PABP2_HUMAN,>sp|Q86U42-2|PABP2_HUMAN". The comma split 2 pro's.
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