[R] new question

[arun]

Hi,


directory<- "/home/arunksa111/dados" #renamed directory to dados
filelist<-function(directory,number,list1){
setwd(directory)
filelist1<-dir(directory)
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE)
list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t",stringsAsFactors=FALSE))
names(list1)<-filelist1
list2<- list(filelist1,list1)
return(list2)
}
foldernames1<-filelist(directory,23,list1)[[1]]
foldernames1
#[1] "a1" "a2" "c1" "c2" "c3" "t1" "t2"
lista<-filelist(directory,23,list1)[[2]] #lista output 

#If you look at the 
 lapply(lista,function(x) sapply(x,class)) #some spec were integer, and some were character
#do this
 listaNew<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))

FacGroup<- c("c1","c3","t2")
#Second function
#f<- function(....)

head(f(listaNew,FacGroup))
#                     Seq        Mod z c1 c3 t2
#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2  0  0  1
#2  aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2  0  0  1
#3       aAAAAAAAAAGAAGGR 1-n_acPro/ 2  0  0  1
#4  aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2  1  0  0
#5            AAAAAAALQAK            2  0  1  1
#6         aAAAAAGAGPEMVR 1-n_acPro/ 2  0  0  2


A.K.



________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 7, 2013 7:12 AM
Subject: Re: new question


Hi.

Sorry again a question about this, but when I run this code I have this error:

Error in `[.data.table`(x1, , `:=`(spec, paste(spec, collapse = ",")),  : 
  Type of RHS ('character') must match LHS ('integer'). To check and coerce would impact performance too much for the fastest cases. Either change the type of the target column, or coerce the RHS of := yourself (e.g. by using 1L instead of 1)

Could you help me to with this? How can I eliminate this?

Thank you




2013/2/28 arun <smartpink111 at yahoo.com>

Hi,
>directory<- "/home/arunksa111/data.new"
>#first function
>filelist<-function(directory,number,list1){
>setwd(directory)
>filelist1<-dir(directory)
>
>direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE)
>list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t",stringsAsFactors=FALSE))
>names(list1)<-filelist1
>list2<- list(filelist1,list1)
>return(list2)
>}
>foldernames1<-filelist(directory,23,list1)[[1]]
>foldernames1
>#[1] "a1" "c1" "c2" "c3" "t1" "t2"
>lista<-filelist(directory,23,list1)[[2]] #lista output
>
>FacGroup<- c("c1","c3","t2")
>
>#Second function
>f<-function(listRes,Toselect){
>res2<-split(listRes,gsub("[0-9]","",names(listRes)))
>res3<-lapply(seq_along(res2),function(i) lapply(res2[[i]],function(x) x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>res4<-lapply(res3,function(x) x[names(x)[names(x)%in%Toselect]])
>res4New<- lapply(res4,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)
>res5<-lapply(res4New,function(x) lapply(x,function(x1){ x1<- data.table(x1);x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))
>res6<- lapply(res5,function(x) lapply(x,function(x1) {x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s", "", unlist(strsplit(x2, ",")))));x3<-as.data.frame(x1);names(x3)[6]<- as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
> 
>res7<-lapply(res6,function(x) Reduce(function(...) merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
> res8<-res7[lapply(res7,length)!=0]
> res9<- Reduce(function(...) merge(...,by=c("Seq","Mod","z"),all=TRUE),res8)
>res9[is.na(res9)] <- 0
>return(res9)
>}
>
>f(lista,FacGroup)
> head(f(lista,FacGroup))
> #                    Seq        Mod z c1 c3 t2
>#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2  0  0  1
>#2  aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2  0  0  1
>#3       aAAAAAAAAAGAAGGR 1-n_acPro/ 2  0  0  1
>#4  aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2  1  0  0
>#5            AAAAAAALQAK            2  0  1  1
>#6         aAAAAAGAGPEMVR 1-n_acPro/ 2  0  0  2
>
>resCounts<- f(lista,FacGroup)
>t.test.p.value <- function(...) {
>    obj<-try(t.test(...), silent=TRUE)
>    if (is(obj, "try-error")) return(NA) else return(obj$p.value)
> }
>
>#3rd function for p-value
>fpv<- function(Countdata){
>resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])), function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else Countdata[i]; colnames(x)<-NULL;x}))
>indx<-combn(names(resNew),2)
>resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i) {x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value)); colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
>resF<-cbind(resCounts,resPval)
>resF
>}
>
>fpv(resCounts)
>
>
>A.K.
>
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta.rt at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Thursday, February 28, 2013 11:30 AM
>Subject: new question
>
>
>
>Sorry about my question, but I need a new small thing...I need to split my function to read data and to do the treatment of the data.
>
>At first I need to know the "names" of the files and read data, and after a new function with my analysis.
>
>So, I did this
>
>directory<-"C:/Users/Vera Costa/Desktop/data.new" 
>filelist<-function(directory,number){
>setwd(directory)
>filelist<-dir(directory)
>return(filelist)
>direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE)
>lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t"))
>names(lista)<-filelist
>return(lista)
>}
>filelist(directory,23)
>
>
>###"a1" "a2" "c1" "c2" "c3" "t1" "t2"
>
>
>
>and after
>
>f<-function(filelist,FacGroup){
>
>res2<-split(lista,names(lista))
> res3<- lapply(res2,function(x) {names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>res3
>#Freq FDR<0.01
> res4<-lapply(seq_along(res3),function(i) lapply(res3[[i]],function(x) x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
> names(res4)<- names(res2)
> res4
>  res4New<-lapply(res4,function(x) lapply(names(x),function(i) do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
> res5<- lapply(res4New,function(x) if(length(x)>1) tail(x,-1) else NULL)
> library(plyr)
> library(data.table)
> res6<- lapply(res5,function(x) lapply(x,function(x1) {x1<-data.table(x1); x1[,spec:=past
>
>
>
>
>How can I "ask lista in second function? Could you help me?             
>