Hi,
Try this:
files<-paste("MSMS_",23,"PepInfo.txt",sep="")
read.data<-function(x) {names(x)<-gsub("^(.*)\\/.*","\\1",x);
lapply(x,function(y) read.table(y,header=TRUE,sep =
"\t",stringsAsFactors=FALSE,fill=TRUE))}
lista<-do.call("c",lapply(list.files(recursive=T)[grep(files,list.files(recursive=T))],read.data))
names(lista)<-paste("group_",gsub("\\d+","",names(lista)),sep="")
res2<-split(lista,names(lista))
res3<- lapply(res2,function(x)
{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
#Freq whole data
res4<-lapply(seq_along(res3),function(i)
do.call(rbind,lapply(res3[[i]],function(x)
as.data.frame(table(factor(x$z,levels=1:3))))))
names(res4)<- names(res2)
library(reshape2)
freq.i1<-do.call(rbind,lapply(res4,function(x)
dcast(melt(data.frame(id=gsub("\\..*","",row.names(x)),x),id.var=c("id","Var1")),id~Var1,value.var="value")))
freq.i1
# id 1 2 3
#group_a a1 1 12 6
#group_c.1 c1 0 10 3
#group_c.2 c2 0 12 3
#group_c.3 c3 0 13 4
#group_t.1 t1 0 10 4
#group_t.2 t2 1 12 6
freq.rel.i1<- as.matrix(freq.i1[,-1]/rowSums(freq.i1[,-1]) )
freq.rel.i1
# 1 2 3
#group_a 0.05263158 0.6315789 0.3157895
#group_c.1 0.00000000 0.7692308 0.2307692
#group_c.2 0.00000000 0.8000000 0.2000000
#group_c.3 0.00000000 0.7647059 0.2352941
#group_t.1 0.00000000 0.7142857 0.2857143
#group_t.2 0.05263158 0.6315789 0.3157895
#Freq with FDR< 0.01
res5<-lapply(seq_along(res3),function(i)
do.call(rbind,lapply(res3[[i]],function(x)
as.data.frame(table(factor(x$z[x[["FDR"]]<0.01],levels=1:3))))))
names(res5)<- names(res2)
freq.f1<- do.call(rbind,lapply(res5,function(x)
dcast(melt(data.frame(id=gsub("\\..*","",row.names(x)),x),id.var=c("id","Var1")),id~Var1,value.var="value")))
freq.f1
# id 1 2 3
#group_a a1 1 10 5
#group_c.1 c1 0 7 2
#group_c.2 c2 0 8 2
#group_c.3 c3 0 6 4
#group_t.1 t1 0 7 4
#group_t.2 t2 1 10 5
freq.rel.f1<- as.matrix(freq.f1[,-1]/rowSums(freq.f1[,-1]))
colour<-sample(rainbow(nrow(freq.rel.i1)))
par(mfrow=c(1,2))
barplot(freq.rel.i1,beside=T,main=("Sample"),xlab="Charge",ylab="Relative
Frequencies",col=colour,legend.text = rownames(freq.rel.i1))
barplot(freq.rel.f1,beside=T,main=("Sample with
FDR<0.01"),xlab="Charge",ylab="Relative Frequencies",col=colour,legend.text =
rownames(freq.rel.f1))
#change the legend position
Also, didn't check the rest of the code from chisquare test.
A.K.
________________________________
From: Vera Costa <veracosta...@gmail.com>
To: arun <smartpink...@yahoo.com>
Sent: Tuesday, February 19, 2013 4:19 PM
Subject: Re: reading data
Here is the code and some outputs.
z.plot <- function(directory,number) {
#reading data
setwd(directory)
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
directT <- direct[grepl("^t", direct)]
directC <- direct[grepl("^c", direct)]
lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t"))
listaC<-lapply(directC, function(x) read.table(x,header=TRUE, sep = "\t"))
listaT<-lapply(directT, function(x) read.table(x,header=TRUE, sep = "\t"))
#count different z values
cab <- vector()
for (i in 1:length(lista)) {
dc<-lista[[i]][ifelse(lista[[i]]$FDR<0.01, TRUE, FALSE),]
dc<-table(dc$z)
cab <- c(cab, names(dc))
}
#Relative freqs to construct the graph
cab <- unique(cab)
print(cab)
###[1] "2" "3" "1"
d <- matrix(ncol=length(cab))
dci<- d[-1,]
dcf <- d[-1,]
dti <- d[-1,]
dtf <- d[-1,]
for (i in 1:length(listaC)) {
#Relative freq of all data
dcc<-listaC[[i]]
dcc<-table(factor(dcc$z, levels=cab))
dci<- rbind(dci, dcc)
rownames(dci)<-rownames(1:(nrow(dci)), do.NULL = FALSE, prefix = "c")
#Relative freq of data with FDR<0.01
dcc1<-listaC[[i]][ifelse(listaC[[i]]$FDR<0.01, TRUE, FALSE),]
dcc1<-table(factor(dcc1$z, levels=cab))
dcf<- rbind(dcf,dcc1)
rownames(dcf)<-rownames(1:(nrow(dcf)), do.NULL = FALSE, prefix = "c")
}
for (i in 1:length(listaT)) {
#Relative freq of all data
dct<-listaT[[i]]
dct<-table(factor(dct$z, levels=cab))
dti<- rbind(dti, dct)
rownames(dti)<-rownames(1:(nrow(dti)), do.NULL = FALSE, prefix = "t")
#Relative freq of data with FDR<0.01
dct1<-listaT[[i]][ifelse(listaT[[i]]$FDR<0.01, TRUE, FALSE),]
dct1<-table(factor(dct1$z, levels=cab))
dtf<- rbind(dtf,dct1)
rownames(dtf)<-rownames(1:(nrow(dtf)), do.NULL = FALSE, prefix = "t")
}
freq.i<-rbind(dci,dti)
freq.f<-rbind(dcf,dtf)
freq.rel.i<-freq.i/apply(freq.i,1,sum)
freq.rel.f<-freq.f/apply(freq.f,1,sum)
print(freq.i)
## 2 3 1
#c1 10 3 0
#c2 12 3 0
#c3 13 4 0
#t1 10 4 0
#t2 12 6 1
print(freq.f)
### 2 3 1
#c1 7 2 0
#c2 8 2 0
#c3 6 4 0
#t1 7 4 0
#t2 10 5 1
print(freq.rel.i)
### 2 3 1
#c1 0.7692308 0.2307692 0.00000000
#c2 0.8000000 0.2000000 0.00000000
#c3 0.7647059 0.2352941 0.00000000
#t1 0.7142857 0.2857143 0.00000000
#t2 0.6315789 0.3157895 0.05263158
print(freq.rel.f)
### 2 3 1
#c1 0.7777778 0.2222222 0.0000
#c2 0.8000000 0.2000000 0.0000
#c3 0.6000000 0.4000000 0.0000
#t1 0.6363636 0.3636364 0.0000
#t2 0.6250000 0.3125000 0.0625
#Graph plot
colour<-sample(rainbow(nrow(freq.rel.i)))
par(mfrow=c(1,2))
barplot(freq.rel.i,beside=T,main=("Sample"),xlab="Charge",ylab="Relative
Frequencies",col=colour,legend.text = rownames(freq.rel.i))
barplot(freq.rel.f,beside=T,main=("Sample with
FDR<0.01"),xlab="Charge",ylab="Relative Frequencies",col=colour,legend.text =
rownames(freq.rel.f))
#average of the group (except c1&t1)
freqs<-rbind(dcf[-1,], dtf[-1,])
average<-apply(freqs,2,mean)
print(average)
### 2 3 1
#8.0000000 3.6666667 0.3333333
#chisquare test function
chisq.test<-function(x,y){
somax<-sum(x)
somay<-sum(y)
nj.<-x+y
nj<-sum(nj.)
ejx<-(nj./nj)*somax
ejy<-(nj./nj)*somay
ETx<-((x-ejx)^2)/ejx
ETy<-((y-ejy)^2)/ejy
ETobs<-sum(ETx)+sum(ETy)
pvalue<-1-pchisq(c(ETobs),df=length(x|y)-1,lower.tail=TRUE)
return(pvalue)
}
#pvalues of the chisquare test between sample and average (H0: two samples has
the same distribution)
pvalues<-c()
for (i in 1:(nrow(freqs))){
a<-chisq.test(freqs[i,],average)
pvalues<-c(pvalues,a)
}
#data frame with final p-values
dataframe<-data.frame(c(rownames(freqs)), c(pvalues))
colnames(dataframe)<-c("sample name","pvalue")
print(dataframe)
### sample name pvalue
#1 c2 0.7235907
#2 c3 0.7963287
#3 0.9079200
}
z.plot("C:/Users/Vera Costa/Desktop/dados",23)
###and two barplots..
Here, I remove the group a1.
Thank you
2013/2/19 arun <smartpink...@yahoo.com>
Hi,
>
>Could you send the results for the folder that was sent to me? It will be
>easy for me.
>
>Arun
>
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta...@gmail.com>
>To: arun <smartpink...@yahoo.com>
>Sent: Tuesday, February 19, 2013 3:47 PM
>
>Subject: Re: reading data
>
>
>Oh sorry, I change the folder.
>
>I send for your folder
>
>
>
>2013/2/19 arun <smartpink...@yahoo.com>
>
>Hello,
>>
>>
>> Regarding the results, is it from the same folder that you sent to me??
>>I am getting different results by running your steps.
>>
>>
>>direct<- list.files(recursive=TRUE)
>> direct
>>#[1] "a1/MSMS_23PepInfo.txt" "c1/MSMS_23PepInfo.txt" "c2/MSMS_23PepInfo.txt"
>>#[4] "c3/MSMS_23PepInfo.txt" "t1/MSMS_23PepInfo.txt" "t2/MSMS_23PepInfo.txt"
>>
>> directT<- list.files(recursive=TRUE)[grepl("^t",dir())]
>>
>>directT
>>#[1] "t1/MSMS_23PepInfo.txt" "t2/MSMS_23PepInfo.txt"
>>
>>
>>directC<- list.files(recursive=TRUE)[grepl("^c",dir())]
>>
>>directC
>>#[1] "c1/MSMS_23PepInfo.txt" "c2/MSMS_23PepInfo.txt" "c3/MSMS_23PepInfo.txt"
>>
>>
>>
>>lista<- lapply(direct,function(x)
>>read.table(x,header=TRUE,stringsAsFactors=FALSE,sep="\t",fill=TRUE))
>>
>>listaT<-lapply(directT, function(x) read.table(x,header=TRUE, sep =
>>"\t",fill=TRUE))
>>listaC<-lapply(directC, function(x) read.table(x,header=TRUE, sep =
>>"\t",fill=TRUE))
>>
>> #count different z values
>> cab <- vector()
>> for (i in 1:length(lista)) {
>> dc<-lista[[i]][ifelse(lista[[i]]$FDR<0.01, TRUE, FALSE),]
>> dc<-table(dc$z)
>> cab <- c(cab, names(dc))
>> }
>>
>> #Relative freqs to construct the graph
>> cab <- unique(cab)
>> print(cab)
>>
>>#[1] "1" "2" "3" #Here results are not correct
>>
>>
>>d <- matrix(ncol=length(cab))
>> dci<- d[-1,]
>> dcf <- d[-1,]
>> dti <- d[-1,]
>> dtf <- d[-1,]
>>
>> for (i in 1:length(listaC)) {
>>
>> #Relative freq of all data
>> dcc<-listaC[[i]]
>> dcc<-table(factor(dcc$z, levels=cab))
>> dci<- rbind(dci, dcc)
>> rownames(dci)<-rownames(1:(nrow(dci)), do.NULL = FALSE, prefix = "c")
>>
>>
>> #Relative freq of data with FDR<0.01
>> dcc1<-listaC[[i]][ifelse(listaC[[i]]$FDR<0.01, TRUE, FALSE),]
>> dcc1<-table(factor(dcc1$z, levels=cab))
>> dcf<- rbind(dcf,dcc1)
>> rownames(dcf)<-rownames(1:(nrow(dcf)), do.NULL = FALSE, prefix = "c")
>> }
>> print(dci) #here too.
>>
>># 1 2 3
>>#c1 0 10 3
>>#c2 0 12 3
>>#c3 0 13 4
>>
>>
>>It is important to clear this before I make any changes to the script. You
>>need to send me the output of the same data folder to understand what is
>>going on.
>>
>>
>>Arun
>>________________________________
>>From: Vera Costa <veracosta...@gmail.com>
>>To: arun <smartpink...@yahoo.com>
>>Sent: Tuesday, February 19, 2013 9:24 AM
>>
>>Subject: Re: reading data
>>
>>
>>Ok.
>>
>>Here is the code and some outputs.
>>
>>z.plot <- function(directory,number) {
>> #reading data
>> setwd(directory)
>> direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
>>full.names = FALSE, recursive = TRUE)
>> directT <- direct[grepl("^t", direct)]
>> directC <- direct[grepl("^c", direct)]
>>
>> lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t"))
>> listaC<-lapply(directC, function(x) read.table(x,header=TRUE, sep = "\t"))
>> listaT<-lapply(directT, function(x) read.table(x,header=TRUE, sep = "\t"))
>>
>> #count different z values
>> cab <- vector()
>> for (i in 1:length(lista)) {
>> dc<-lista[[i]][ifelse(lista[[i]]$FDR<0.01, TRUE, FALSE),]
>> dc<-table(dc$z)
>> cab <- c(cab, names(dc))
>> }
>>
>> #Relative freqs to construct the graph
>> cab <- unique(cab)
>> print(cab)
>>
>>###[1] "1" "2" "3" "4" "5"
>>
>>
>>
>> d <- matrix(ncol=length(cab))
>> dci<- d[-1,]
>> dcf <- d[-1,]
>> dti <- d[-1,]
>> dtf <- d[-1,]
>>
>> for (i in 1:length(listaC)) {
>>
>> #Relative freq of all data
>> dcc<-listaC[[i]]
>> dcc<-table(factor(dcc$z, levels=cab))
>> dci<- rbind(dci, dcc)
>> rownames(dci)<-rownames(1:(nrow(dci)), do.NULL = FALSE, prefix = "c")
>>
>>
>> #Relative freq of data with FDR<0.01
>> dcc1<-listaC[[i]][ifelse(listaC[[i]]$FDR<0.01, TRUE, FALSE),]
>> dcc1<-table(factor(dcc1$z, levels=cab))
>> dcf<- rbind(dcf,dcc1)
>> rownames(dcf)<-rownames(1:(nrow(dcf)), do.NULL = FALSE, prefix = "c")
>> }
>> print(dci)
>>
>>### 1 2 3 4 5
>>#c1 93 8356 3621 450 55
>>#c2 108 13513 6859 793 73
>>#c3 97 13526 6724 739 82
>>#c4 101 13417 6574 761 62
>>
>> print(dcf)
>>
>>### 1 2 3 4 5
>>#c1 10 4576 2100 199 17
>>#c2 7 7831 4039 314 23
>>#c3 16 7887 4087 286 22
>>#c4 20 7824 4045 311 20
>>
>> for (i in 1:length(listaT)) {
>>
>> #Relative freq of all data
>> dct<-listaT[[i]]
>> dct<-table(factor(dct$z, levels=cab))
>> dti<- rbind(dti, dct)
>> rownames(dti)<-rownames(1:(nrow(dti)), do.NULL = FALSE, prefix = "t")
>>
>>
>> #Relative freq of data with FDR<0.01
>> dct1<-listaT[[i]][ifelse(listaT[[i]]$FDR<0.01, TRUE, FALSE),]
>> dct1<-table(factor(dct1$z, levels=cab))
>> dtf<- rbind(dtf,dct1)
>> rownames(dtf)<-rownames(1:(nrow(dtf)), do.NULL = FALSE, prefix = "t")
>> }
>>
>> print(dti)
>>
>>### 1 2 3 4 5
>>#t1 32 8640 4098 429 36
>>#t2 128 13209 6723 788 75
>>#t3 85 13043 6691 754 82
>>#t4 139 13750 7036 807 84
>>
>> print(dtf)
>>
>>
>>#### 1 2 3 4 5
>>#t1 5 4885 2571 196 8
>>#t2 12 7752 4209 360 28
>>#t3 19 7563 4086 336 18
>>#t4 14 8108 4218 312 26
>>
>>
>> freq.i<-rbind(dci,dti)
>> freq.f<-rbind(dcf,dtf)
>> freq.rel.i<-freq.i/apply(freq.i,1,sum)
>> freq.rel.f<-freq.f/apply(freq.f,1,sum)
>> print(freq.i)
>>## 1 2 3 4 5
>>#c1 93 8356 3621 450 55
>>#c2 108 13513 6859 793 73
>>#c3 97 13526 6724 739 82
>>#c4 101 13417 6574 761 62
>>#t1 32 8640 4098 429 36
>>#t2 128 13209 6723 788 75
>>#t3 85 13043 6691 754 82
>>#t4 139 13750 7036 807 84
>>
>> print(freq.f)
>> ### 1 2 3 4 5
>>#c1 10 4576 2100 199 17
>>#c2 7 7831 4039 314 23
>>#c3 16 7887 4087 286 22
>>#c4 20 7824 4045 311 20
>>#t1 5 4885 2571 196 8
>>#t2 12 7752 4209 360 28
>>#t3 19 7563 4086 336 18
>>#t4 14 8108 4218 312 26
>>
>> print(freq.rel.i)
>>### 1 2 3 4 5
>>#c1 0.007395626 0.6644930 0.2879523 0.03578529 0.004373757
>>#c2 0.005059496 0.6330460 0.3213248 0.03714982 0.003419844
>>#c3 0.004582389 0.6389834 0.3176493 0.03491119 0.003873772
>>#c4 0.004829070 0.6415013 0.3143199 0.03638537 0.002964380
>>#t1 0.002417832 0.6528145 0.3096335 0.03241405 0.002720060
>>#t2 0.006117670 0.6313148 0.3213210 0.03766190 0.003584572
>>#t3 0.004115226 0.6314694 0.3239409 0.03650448 0.003969983
>>#t4 0.006371470 0.6302714 0.3225156 0.03699120 0.003850385
>> print(freq.rel.f)
>>
>>### 1 2 3 4 5
>>#c1 0.0014488554 0.6629962 0.3042596 0.02883222 0.002463054
>>#c2 0.0005731128 0.6411495 0.3306861 0.02570820 0.001883085
>>#c3 0.0013010246 0.6413238 0.3323305 0.02325581 0.001788909
>>#c4 0.0016366612 0.6402619 0.3310147 0.02545008 0.001636661
>>#t1 0.0006523157 0.6373125 0.3354207 0.02557078 0.001043705
>>#t2 0.0009707952 0.6271337 0.3405064 0.02912386 0.002265189
>>#t3 0.0015804359 0.6290967 0.3398769 0.02794876 0.001497255
>>#t4 0.0011042751 0.6395330 0.3327023 0.02460956 0.002050797
>>
>>#Graph plot
>>colour<-sample(rainbow(nrow(freq.rel.i)))
>>par(mfrow=c(1,2))
>>barplot(freq.rel.i,beside=T,main=("Sample"),xlab="Charge",ylab="Relative
>>Frequencies",col=colour,legend.text = rownames(freq.rel.i))
>>barplot(freq.rel.f,beside=T,main=("Sample with
>>FDR<0.01"),xlab="Charge",ylab="Relative Frequencies",col=colour,legend.text =
>>rownames(freq.rel.f))
>>
>>#average of the group (except c1&t1)
>>freqs<-rbind(dcf[-1,], dtf[-1,])
>>average<-apply(freqs,2,mean)
>>print(average)
>>
>>### 1 2 3 4 5
>> # 14.66667 7827.50000 4114.00000 319.83333 22.83333
>>
>>#chisquare test function
>>chisq.test<-function(x,y){
>> somax<-sum(x)
>> somay<-sum(y)
>> nj.<-x+y
>> nj<-sum(nj.)
>> ejx<-(nj./nj)*somax
>> ejy<-(nj./nj)*somay
>> ETx<-((x-ejx)^2)/ejx
>> ETy<-((y-ejy)^2)/ejy
>> ETobs<-sum(ETx)+sum(ETy)
>> pvalue<-1-pchisq(c(ETobs),df=length(x|y)-1,lower.tail=TRUE)
>> return(pvalue)
>> }
>>
>>#pvalues of the chisquare test between sample and average (H0: two samples
>>has the same distribution)
>>pvalues<-c()
>>for (i in 1:(nrow(freqs))){
>>a<-chisq.test(freqs[i,],average)
>>pvalues<-c(pvalues,a)
>>}
>>print(pvalues)
>>##[1] 0.5307206 0.6849480 0.8332661 0.3474956 0.5546527 0.9387602
>>
>>#data frame with final p-values
>>dataframe<-data.frame(c(rownames(freqs)), c(pvalues))
>>colnames(dataframe)<-c("sample name","pvalue")
>>print(dataframe)
>>
>>### sample name pvalue
>>#1 c2 0.5307206
>>#2 c3 0.6849480
>>#3 c4 0.8332661
>>#4 t2 0.3474956
>>#5 t3 0.5546527
>>#6 t4 0.9387602
>>}
>>z.plot("C:/Users/Vera Costa/Desktop/dados",23)
>>
>>###and two barplots...
>>
>>Thank you
>>
>>
>>
>>
>>2013/2/19 arun <smartpink...@yahoo.com>
>>
>>Got it.
>>>
>>>So, if I run your codes that you sent yesterday, will I get the correct
>>>results for relative frequency etc. It would be also great if you can sent
>>>me the output generated using your codes (on two groups as you showed
>>>yesterday). It will help me in checking results much faster than running
>>>your code and see if that is the result (because I have to do some
>>>adjustment to your code for running in linux especially the ?dir()).
>>>
>>>I may be able to run it only later.
>>>
>>>Arun
>>>
>>>
>>>
>>>
>>>
>>>
>>>________________________________
>>>From: Vera Costa <veracosta...@gmail.com>
>>>To: arun <smartpink...@yahoo.com>
>>>Sent: Tuesday, February 19, 2013 8:53 AM
>>>
>>>Subject: Re: reading data
>>>
>>>
>>>I sent in second email.
>>>
>>>But I send again.
>>>
>>>
>>>
>>>2013/2/19 arun <smartpink...@yahoo.com>
>>>
>>>
>>>>
>>>>Your attachment didn't came through.
>>>>
>>>>Arun
>>>>
>>>>
>>>>
>>>>
>>>>________________________________
>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>To: arun <smartpink...@yahoo.com>
>>>>Sent: Tuesday, February 19, 2013 8:47 AM
>>>>
>>>>Subject: Re: reading data
>>>>
>>>>
>>>>Sorry about a lot of questions.
>>>>
>>>>I attach a small part of my real data (I have a lot of row).
>>>>
>>>>My main objective is construct two graph. The first with the relative
>>>>frequencies of each group (c1,c2,c3....). The second with the same
>>>>frequencies but with FDR<0.01.
>>>>
>>>>After that I need to do the average in each group (but without the first
>>>>group-c1,t1,a1....) and do the qui square test to see if the groups has the
>>>>same distribution. You understand?
>>>>
>>>>At first, I had only two groups, and I did the code that I sent you. But I
>>>>need a general code, not for two groups that I know the names, but for all
>>>>groups (sometimes I can have 7 or 8 or 9 groups).
>>>>
>>>>it´s better now my explanation? :-)
>>>>My English isn't also very good :-)
>>>>
>>>>Please not publish this data in forum...
>>>>
>>>>Thank you
>>>>
>>>>
>>>>
>>>>
>>>>2013/2/18 arun <smartpink...@yahoo.com>
>>>>
>>>>Hi,
>>>>>
>>>>>I run the codes to understand what was going on.
>>>>>
>>>>>I didn't fully understand it as you constructed the codes for your
>>>>>original dataset and not for the 'data` directory you sent to me.
>>>>>
>>>>>A.K.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>________________________________
>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>To: arun <smartpink...@yahoo.com>
>>>>>Sent: Monday, February 18, 2013 4:02 PM
>>>>>
>>>>>Subject: Re: reading data
>>>>>
>>>>>
>>>>>Thank you.
>>>>>I don't need the same,but equivalent. I will try your suggestions.
>>>>>Thank you.
>>>>>No dia 18 de Fev de 2013 19:41, "arun" <smartpink...@yahoo.com> escreveu:
>>>>>
>>>>>Hi,
>>>>>>I am not able to open your graph. I am using linux.
>>>>>>
>>>>>>Also, the codes in the function are not reproducible
>>>>>> directT <- direct[grepl("^t", direct)]
>>>>>> directC <- direct[grepl("^c", direct)]
>>>>>>
>>>>>>It takes double the time to know what is going on.
>>>>>>
>>>>>>dir()
>>>>>>#[1] "a1" "a2" "a3" "b1" "b2" "c1"
>>>>>>
>>>>>>direct<- list.files(recursive=TRUE)[grepl("^a|^b",dir())]
>>>>>>
>>>>>> direct
>>>>>>#[1] "MSMS_23PepInfo.txt" "MSMS_23PepInfo.txt" "MSMS_23PepInfo.txt"
>>>>>>#[4] "MSMS_23PepInfo.txt" "MSMS_23PepInfo.txt"
>>>>>>directA<- list.files(recursive=TRUE)[grepl("^a",dir())]
>>>>>>directB<- list.files(recursive=TRUE)[grepl("^b",dir())]
>>>>>>lista<- lapply(direct,function(x)
>>>>>>read.table(x,header=TRUE,stringsAsFactors=FALSE,sep="\t",fill=TRUE))
>>>>>>
>>>>>>listaA<-lapply(directA, function(x) read.table(x,header=TRUE, sep =
>>>>>>"\t",fill=TRUE))
>>>>>>listaB<-lapply(directB, function(x) read.table(x,header=TRUE, sep =
>>>>>>"\t",fill=TRUE))
>>>>>>
>>>>>>#here I am changing the names listaT, z, etc..
>>>>>>
>>>>>>count different mm values
>>>>>> cab <- vector()
>>>>>> for (i in 1:length(lista)) {
>>>>>> dc<-lista[[i]][ifelse(lista[[i]]$b<0.01, TRUE, FALSE),]
>>>>>> dc<-table(dc$mm)
>>>>>> cab <- c(cab, names(dc))
>>>>>> }
>>>>>>
>>>>>> #Relative freqs to construct the graph
>>>>>> cab <- unique(cab)
>>>>>> d <- matrix(ncol=length(cab))
>>>>>> dci<- d[-1,]
>>>>>> dcf <- d[-1,]
>>>>>> dti <- d[-1,]
>>>>>> dtf <- d[-1,]
>>>>>>
>>>>>> ########################################
>>>>>> for (i in 1:length(listaA)) {
>>>>>>
>>>>>> #Relative freq of all data
>>>>>> dcc<-listaA[[i]]
>>>>>> dcc<-table(factor(dcc$mm, levels=cab))
>>>>>> dci<- rbind(dci, dcc)
>>>>>> rownames(dci)<-rownames(1:(nrow(dci)), do.NULL = FALSE, prefix = "a")
>>>>>>
>>>>>>
>>>>>> #Relative freq of data with FDR<0.01
>>>>>> dcc1<-listaA[[i]][ifelse(listaA[[i]]$FDR<0.01, TRUE, FALSE),]
>>>>>> dcc1<-table(factor(dcc1$mm, levels=cab))
>>>>>> dcf<- rbind(dcf,dcc1)
>>>>>> rownames(dcf)<-rownames(1:(nrow(dcf)), do.NULL = FALSE, prefix = "a")
>>>>>> }
>>>>>>
>>>>>> for (i in 1:length(listaB)) {
>>>>>>
>>>>>> #Relative freq of all data
>>>>>> dct<-listaB[[i]]
>>>>>> dct<-table(factor(dct$mm, levels=cab))
>>>>>> dti<- rbind(dti, dct)
>>>>>> rownames(dti)<-rownames(1:(nrow(dti)), do.NULL = FALSE, prefix = "b")
>>>>>>
>>>>>>
>>>>>> #Relative freq of data with FDR<0.01
>>>>>> dct1<-listaB[[i]][ifelse(listaB[[i]]$FDR<0.01, TRUE, FALSE),]
>>>>>> dct1<-table(factor(dct1$mm, levels=cab))
>>>>>> dtf<- rbind(dtf,dct1)
>>>>>> rownames(dtf)<-rownames(1:(nrow(dtf)), do.NULL = FALSE, prefix = "b")
>>>>>> }
>>>>>> freq.i<-rbind(dci,dti)
>>>>>> freq.f<-rbind(dcf,dtf)
>>>>>> freq.rel.i<-freq.i/apply(freq.i,1,sum)
>>>>>> freq.rel.f<-freq.f/apply(freq.f,1,sum)
>>>>>>
>>>>>>
>>>>>> freq.i
>>>>>># 2 3
>>>>>>#a1 4 1
>>>>>>#a2 4 1
>>>>>>#a3 4 1
>>>>>>#b1 4 1
>>>>>>#b2 4 1
>>>>>>#b3 4 1
>>>>>>#b4 4 1
>>>>>>#result from my code.
>>>>>> files<-paste("MSMS_",23,"PepInfo.txt",sep="")
>>>>>>read.data<-function(x) {names(x)<-gsub("^(.*)\\/.*","\\1",x);
>>>>>>lapply(x,function(y) read.table(y,header=TRUE,sep =
>>>>>>"\t",stringsAsFactors=FALSE,fill=TRUE))}
>>>>>>lista<-do.call("c",lapply(list.files(recursive=T)[grep(files,list.files(recursive=T))],read.data))
>>>>>>names(lista)<-paste("group_",gsub("\\d+","",names(lista)),sep="")
>>>>>>
>>>>>>res2<-split(lista,names(lista))
>>>>>>res3<- lapply(res2,function(x)
>>>>>>{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>>>>>>res4<-lapply(seq_along(res3),function(i) do.call(rbind,lapply(res3[[i]],
>>>>>>function(x) table(x$mm[x[["b"]]<0.01]))))
>>>>>> names(res4)<- names(res2)
>>>>>>
>>>>>>
>>>>>>res4
>>>>>>$group_a
>>>>>># 2 3
>>>>>>#a1 3 1
>>>>>>#a2 3 1
>>>>>>#a3 3 1
>>>>>>
>>>>>>#$group_b
>>>>>> # 2 3
>>>>>>#b1 3 1
>>>>>>#b2 3 1
>>>>>>
>>>>>>#$group_c
>>>>>> # 2 3
>>>>>>#c1 3 1
>>>>>>
>>>>>>There is a difference in output from freq.i and res4. There were only
>>>>>>two files under 'group_b`. So, check your codes.
>>>>>>A.K.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>________________________________
>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>Sent: Monday, February 18, 2013 10:27 AM
>>>>>>Subject: Re: reading data
>>>>>>
>>>>>>
>>>>>>Hi!!!
>>>>>>
>>>>>>I'm coming to ask a new question.
>>>>>>
>>>>>>I want a function to do my statistics. I start with you had send me:
>>>>>>
>>>>>>z.plot <- function(directory,number) {
>>>>>> setwd(directory)
>>>>>> indx<-gsub("[./]","",list.dirs())
>>>>>> indx1<- indx[indx!=""]
>>>>>> print(indx1)
>>>>>> files<-paste("MSMS_",number,"PepInfo.txt",sep="")
>>>>>> read.data<-function(x) {names(x)<-gsub("^(.*)\\/.*","\\1",x);
>>>>>>lapply(x,function(y) read.table(y,header=TRUE,sep =
>>>>>>"\t",stringsAsFactors=FALSE,fill=TRUE))}
>>>>>>
>>>>>>lista<-do.call("c",lapply(list.files(recursive=T)[grep(files,list.files(recursive=T))],read.data))
>>>>>> print(lista)
>>>>>> #names(lista)<-paste("group_",gsub("\\d+","",names(lista)),sep="") ve =
>>>>>>TRUE)
>>>>>> }
>>>>>>z.plot("C:/Users/Vera Costa/Desktop/dados.lixo",23)
>>>>>>
>>>>>>
>>>>>>In my lista I can´t merge rows to have the group, because the idea is for
>>>>>>each file count frequencies of mm, when b<0.01. after that I want a
>>>>>>graph like the graph in attach.
>>>>>>
>>>>>>
>>>>>>When I had 2 groups and knew the name of the groups, I did the code (but
>>>>>>Know I have more groups and, maybe, I don´t know the name of the groups):
>>>>>>
>>>>>>z.plot <- function(directory,number) {
>>>>>> #reading data
>>>>>> setwd(directory)
>>>>>> direct<-dir(directory,pattern =
>>>>>>paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive
>>>>>>= TRUE)
>>>>>> directT <- direct[grepl("^t", direct)]
>>>>>> directC <- direct[grepl("^c", direct)]
>>>>>>
>>>>>> lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep = "\t"))
>>>>>> listaC<-lapply(directC, function(x) read.table(x,header=TRUE, sep =
>>>>>>"\t"))
>>>>>> listaT<-lapply(directT, function(x) read.table(x,header=TRUE, sep =
>>>>>>"\t"))
>>>>>>
>>>>>> #count different z values
>>>>>> cab <- vector()
>>>>>> for (i in 1:length(lista)) {
>>>>>> dc<-lista[[i]][ifelse(lista[[i]]$FDR<0.01, TRUE, FALSE),]
>>>>>> dc<-table(dc$z)
>>>>>> cab <- c(cab, names(dc))
>>>>>> }
>>>>>>
>>>>>> #Relative freqs to construct the graph
>>>>>> cab <- unique(cab)
>>>>>> d <- matrix(ncol=length(cab))
>>>>>> dci<- d[-1,]
>>>>>> dcf <- d[-1,]
>>>>>> dti <- d[-1,]
>>>>>> dtf <- d[-1,]
>>>>>>
>>>>>> for (i in 1:length(listaC)) {
>>>>>>
>>>>>> #Relative freq of all data
>>>>>> dcc<-listaC[[i]]
>>>>>> dcc<-table(factor(dcc$z, levels=cab))
>>>>>> dci<- rbind(dci, dcc)
>>>>>> rownames(dci)<-rownames(1:(nrow(dci)), do.NULL = FALSE, prefix = "c")
>>>>>>
>>>>>>
>>>>>> #Relative freq of data with FDR<0.01
>>>>>> dcc1<-listaC[[i]][ifelse(listaC[[i]]$FDR<0.01, TRUE, FALSE),]
>>>>>> dcc1<-table(factor(dcc1$z, levels=cab))
>>>>>> dcf<- rbind(dcf,dcc1)
>>>>>> rownames(dcf)<-rownames(1:(nrow(dcf)), do.NULL = FALSE, prefix = "c")
>>>>>> }
>>>>>>
>>>>>> for (i in 1:length(listaT)) {
>>>>>>
>>>>>> #Relative freq of all data
>>>>>> dct<-listaT[[i]]
>>>>>> dct<-table(factor(dct$z, levels=cab))
>>>>>> dti<- rbind(dti, dct)
>>>>>> rownames(dti)<-rownames(1:(nrow(dti)), do.NULL = FALSE, prefix = "t")
>>>>>>
>>>>>>
>>>>>> #Relative freq of data with FDR<0.01
>>>>>> dct1<-listaT[[i]][ifelse(listaT[[i]]$FDR<0.01, TRUE, FALSE),]
>>>>>> dct1<-table(factor(dct1$z, levels=cab))
>>>>>> dtf<- rbind(dtf,dct1)
>>>>>> rownames(dtf)<-rownames(1:(nrow(dtf)), do.NULL = FALSE, prefix = "t")
>>>>>> }
>>>>>> freq.i<-rbind(dci,dti)
>>>>>> freq.f<-rbind(dcf,dtf)
>>>>>> freq.rel.i<-freq.i/apply(freq.i,1,sum)
>>>>>> freq.rel.f<-freq.f/apply(freq.f,1,sum)
>>>>>>
>>>>>>#Graph plot
>>>>>>colour<-sample(rainbow(nrow(freq.rel.i)))
>>>>>>par(mfrow=c(1,2))
>>>>>>barplot(freq.rel.i,beside=T,main=("Sample"),xlab="Charge",ylab="Relative
>>>>>>Frequencies",col=colour,legend.text = rownames(freq.rel.i))
>>>>>>barplot(freq.rel.f,beside=T,main=("Sample with
>>>>>>FDR<0.01"),xlab="Charge",ylab="Relative
>>>>>>Frequencies",col=colour,legend.text = rownames(freq.rel.f))
>>>>>>#average of the group (except c1&t1)
>>>>>>freqs<-rbind(dcf[-1,], dtf[-1,])
>>>>>>average<-apply(freqs,2,mean)
>>>>>>
>>>>>>#chisquare test function
>>>>>>chisq.test<-function(x,y){
>>>>>> somax<-sum(x)
>>>>>> somay<-sum(y)
>>>>>> nj.<-x+y
>>>>>> nj<-sum(nj.)
>>>>>> ejx<-(nj./nj)*somax
>>>>>> ejy<-(nj./nj)*somay
>>>>>> ETx<-((x-ejx)^2)/ejx
>>>>>> ETy<-((y-ejy)^2)/ejy
>>>>>> ETobs<-sum(ETx)+sum(ETy)
>>>>>> pvalue<-1-pchisq(c(ETobs),df=length(x|y)-1,lower.tail=TRUE)
>>>>>> return(pvalue)
>>>>>> }
>>>>>>
>>>>>>#pvalues of the chisquare test between sample and average (H0: two
>>>>>>samples has the same distribution)
>>>>>>pvalues<-c()
>>>>>>for (i in 1:(nrow(freqs))){
>>>>>>a<-chisq.test(freqs[i,],average)
>>>>>>pvalues<-c(pvalues,a)
>>>>>>}
>>>>>>#data frame with final p-values
>>>>>>dataframe<-data.frame(c(rownames(freqs)), c(pvalues))
>>>>>>colnames(dataframe)<-c("sample name","pvalue")
>>>>>>print(dataframe)
>>>>>>}
>>>>>>z.plot("C:/Users/Vera/Desktop/data",23)
>>>>>>
>>>>>>
>>>>>>
>>>>>>Thank you again
>>>>>>
>>>>>>
>>>>>>
>>>>>>2013/2/17 arun <smartpink...@yahoo.com>
>>>>>>
>>>>>>HI Vera,
>>>>>>>
>>>>>>>No problem. I am cc:ing to r-help.
>>>>>>>
>>>>>>>A.K.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>________________________________
>>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>>Sent: Sunday, February 17, 2013 5:44 AM
>>>>>>>Subject: Re: reading data
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Hi. Thank you. It works now:-)
>>>>>>>And yes, I use windows.
>>>>>>>Thank you very much.
>>>>>>>No dia 17 de Fev de 2013 00:44, "arun" <smartpink...@yahoo.com> escreveu:
>>>>>>>
>>>>>>>Hi Vera,
>>>>>>>>
>>>>>>>>Have you tried the suggestion?
>>>>>>>>
>>>>>>>>Are you using Windows?
>>>>>>>>Thanks,
>>>>>>>>Arun
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>________________________________
>>>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>>>Sent: Saturday, February 16, 2013 7:10 PM
>>>>>>>>Subject: Re: reading data
>>>>>>>>
>>>>>>>>
>>>>>>>>Thank you.
>>>>>>>>In mine, I have an error " 'what' must be a character string or a
>>>>>>>>function".
>>>>>>>>I need to do equivalent in my system.
>>>>>>>>Thank you and sorry one more time.
>>>>>>>>No dia 16 de Fev de 2013 23:53, "arun" <smartpink...@yahoo.com>
>>>>>>>>escreveu:
>>>>>>>>
>>>>>>>>Hi,
>>>>>>>>>You didn't mention what the error message or whether you are reading
>>>>>>>>>file names which are not "mmmmm11kk.txt".
>>>>>>>>>
>>>>>>>>>It is workiing on my system as I run it again.
>>>>>>>>>?c() combine values into a vector or list.
>>>>>>>>>
>>>>>>>>> sessionInfo()
>>>>>>>>>R version 2.15.1 (2012-06-22)
>>>>>>>>>Platform: x86_64-pc-linux-gnu (64-bit)
>>>>>>>>>
>>>>>>>>>locale:
>>>>>>>>> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
>>>>>>>>> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
>>>>>>>>> [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
>>>>>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>>>>>[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>>>>>>>>>
>>>>>>>>>attached base packages:
>>>>>>>>>[1] stats graphics grDevices utils datasets methods base
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>other attached packages:
>>>>>>>>>[1] stringr_0.6.2 reshape2_1.2.2
>>>>>>>>>
>>>>>>>>>loaded via a namespace (and not attached):
>>>>>>>>>[1] plyr_1.8
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>#code
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>res<-do.call(c,lapply(list.files(recursive=T)[grep("mmmmm11kk",list.files(recursive=T))],function(x)
>>>>>>>>> {names(x)<-gsub("^(.*)\\/.*","\\1",x); lapply(x,function(y)
>>>>>>>>>read.table(y,header=TRUE,stringsAsFactors=FALSE,fill=TRUE))})) #it
>>>>>>>>>seems like one of the rows of your file doesn't have 6 elements, so
>>>>>>>>>added fill=TRUE
>>>>>>>>> names(res)<-paste("group_",gsub("\\d+","",names(res)),sep="")
>>>>>>>>>res2<-split(res,names(res))
>>>>>>>>>res3<- lapply(res2,function(x)
>>>>>>>>>{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>>>>>>>>>#result
>>>>>>>>>
>>>>>>>>>res3
>>>>>>>>>#$group_a
>>>>>>>>>#$group_a$a1
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>$group_a$a2
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>$group_a$a3
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>$group_b
>>>>>>>>>$group_b$b1
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>$group_b$b2
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>$group_c
>>>>>>>>>$group_c$c1
>>>>>>>>> Id M mm x b u k j y p v
>>>>>>>>>1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>A.K.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>________________________________
>>>>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>>>>Sent: Saturday, February 16, 2013 6:32 PM
>>>>>>>>>Subject: Re: reading data
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>Sorry again... In:
>>>>>>>>>res<-do.call(c,lapply(list.files(recursive=T)[grep("...
>>>>>>>>>What is this c? In do.call(c, When I put this row im R, I have an
>>>>>>>>>error.
>>>>>>>>>Thank you
>>>>>>>>>No dia 15 de Fev de 2013 18:11, "arun" <smartpink...@yahoo.com>
>>>>>>>>>escreveu:
>>>>>>>>>
>>>>>>>>>Hi,
>>>>>>>>>>No problem.
>>>>>>>>>>
>>>>>>>>>>BTW, these questions are not stupid..
>>>>>>>>>>Arun
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>________________________________
>>>>>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>>>>>Sent: Friday, February 15, 2013 1:08 PM
>>>>>>>>>>Subject: Re: reading data
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Thank you very much.
>>>>>>>>>>
>>>>>>>>>>I will try to apply and after I tell you if it is ok :-)
>>>>>>>>>>
>>>>>>>>>>Thank you and sorry about this questions (sometimes stupid questions).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>2013/2/15 arun <smartpink...@yahoo.com>
>>>>>>>>>>
>>>>>>>>>>HI,
>>>>>>>>>>>No problem.
>>>>>>>>>>>?c() for concatenate to vector or list().
>>>>>>>>>>>If I use do.call(cbind,..) or do.call(rbind,...)
>>>>>>>>>>>
>>>>>>>>>>>do.call(cbind,lapply(list.files(recursive=T)[grep("mmmmm11kk",list.files(recursive=T))],function(x)
>>>>>>>>>>> {names(x)<-gsub("^(.*)\\/.*","\\1",x); lapply(x,function(y)
>>>>>>>>>>>read.table(y,header=TRUE,stringsAsFactors=FALSE,fill=TRUE))}))
>>>>>>>>>>># [,1] [,2] [,3] [,4] [,5] [,6]
>>>>>>>>>>>#a1 List,11 List,11 List,11 List,11 List,11 List,11
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>do.call(rbind,lapply(list.files(recursive=T)[grep("mmmmm11kk",list.files(recursive=T))],function(x)
>>>>>>>>>>> {names(x)<-gsub("^(.*)\\/.*","\\1",x); lapply(x,function(y)
>>>>>>>>>>>read.table(y,header=TRUE,stringsAsFactors=FALSE,fill=TRUE))}))
>>>>>>>>>>># a1
>>>>>>>>>>>#[1,] List,11
>>>>>>>>>>>#[2,] List,11
>>>>>>>>>>>#[3,] List,11
>>>>>>>>>>>#[4,] List,11
>>>>>>>>>>>#[5,] List,11
>>>>>>>>>>>#[6,] List,11
>>>>>>>>>>>ie.
>>>>>>>>>>>list within in a list
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>restrial<-lapply(list.files(recursive=T)[grep("mmmmm11kk",list.files(recursive=T))],function(x)
>>>>>>>>>>> {names(x)<-gsub("^(.*)\\/.*","\\1",x); lapply(x,function(y)
>>>>>>>>>>>read.table(y,header=TRUE,stringsAsFactors=FALSE,fill=TRUE))})
>>>>>>>>>>> str(restrial)
>>>>>>>>>>>#List of 6
>>>>>>>>>>># $ :List of 1
>>>>>>>>>>> #..$ a1:'data.frame': 6 obs. of 11 variables:
>>>>>>>>>>> .#. ..$ Id: chr [1:6] "aAA" "aAAAA" "aA" "aAA" ...
>>>>>>>>>>> #.. ..$ M : chr [1:6] "1" "1" "2" "1" ...
>>>>>>>>>>> #. ..$ mm: int [1:6] 2 2 1 2 3 2
>>>>>>>>>>> #. ..$ x : int [1:6] 739 2263 1 1965 3660 1972
>>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>>str(res)
>>>>>>>>>>>#List of 6
>>>>>>>>>>># $ a1:'data.frame': 6 obs. of 11 variables:
>>>>>>>>>>> # ..$ Id: chr [1:6] "aAA" "aAAAA" "aA" "aAA" ...
>>>>>>>>>>> #..$ M : chr [1:6] "1" "1" "2" "1" ...
>>>>>>>>>>> # ..$ mm: int [1:6] 2 2 1 2 3 2
>>>>>>>>>>> # ..$ x : int [1:6] 739 2263 1 1965 3660 1972
>>>>>>>>>>>-----------------------------------------------------------------
>>>>>>>>>>>
>>>>>>>>>>>You mentioned about naming this to "group_a","group_b". etc..
>>>>>>>>>>>
>>>>>>>>>>> names(res)<-paste("group_",gsub("\\d+","",names(res)),sep="")
>>>>>>>>>>>res2<-split(res,names(res))
>>>>>>>>>>>
>>>>>>>>>>>res3<- lapply(res2,function(x)
>>>>>>>>>>>{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>>>>>>>>>>> res3$group_a
>>>>>>>>>>>$a1
>>>>>>>>>>>
>>>>>>>>>>># Id M mm x b u k j y p v
>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>
>>>>>>>>>>>#$a2
>>>>>>>>>>>
>>>>>>>>>>># Id M mm x b u k j y p v
>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>
>>>>>>>>>>>#$a3
>>>>>>>>>>>
>>>>>>>>>>> # Id M mm x b u k j y p v
>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>A.K.
>>>>>>>>>>>
>>>>>>>>>>>________________________________
>>>>>>>>>>>From: Vera Costa <veracosta...@gmail.com>
>>>>>>>>>>>To: arun <smartpink...@yahoo.com>
>>>>>>>>>>>Sent: Friday, February 15, 2013 12:39 PM
>>>>>>>>>>>Subject: Re: reading data
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>Thank you very much and sorry my questions.
>>>>>>>>>>>
>>>>>>>>>>>But this code isn't grouping for letters sure? I mean, a1,a2,a3 is
>>>>>>>>>>>the same group, (the first letter give me the name of the group)
>>>>>>>>>>>
>>>>>>>>>>>Another question, in do.call, you did do.call (c,.....) .What is c?
>>>>>>>>>>>
>>>>>>>>>>>Sorry
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>2013/2/15 arun <smartpink...@yahoo.com>
>>>>>>>>>>>
>>>>>>>>>>>HI,
>>>>>>>>>>>>
>>>>>>>>>>>>Just to add:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>res<-do.call(c,lapply(list.files(recursive=T)[grep("mmmmm11kk",list.files(recursive=T))],function(x)
>>>>>>>>>>>> {names(x)<-gsub("^(.*)\\/.*","\\1",x); lapply(x,function(y)
>>>>>>>>>>>>read.table(y,header=TRUE,stringsAsFactors=FALSE,fill=TRUE))})) #it
>>>>>>>>>>>>seems like one of the rows of your file doesn't have 6 elements, so
>>>>>>>>>>>>added fill=TRUE
>>>>>>>>>>>>
>>>>>>>>>>>> names(res)<-paste("group_",gsub("\\d+","",names(res)),sep="")
>>>>>>>>>>>>res[grep("group_b",names(res))]
>>>>>>>>>>>>
>>>>>>>>>>>>I am not sure how you want the grouped data to look like. If you
>>>>>>>>>>>>want something like this:
>>>>>>>>>>>>res1<-do.call(rbind,res)
>>>>>>>>>>>>res2<-lapply(split(res1,gsub("[.0-9]","",row.names(res1))),function(x)
>>>>>>>>>>>> {row.names(x)<-1:nrow(x);x})
>>>>>>>>>>>>res2
>>>>>>>>>>>>#$group_a
>>>>>>>>>>>>
>>>>>>>>>>>> # Id M mm x b u k j y p v
>>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>#7 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#8 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#9 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#10 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#11 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#12 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>#13 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#14 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#15 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#16 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#17 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#18 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>#$group_b
>>>>>>>>>>>> # Id M mm x b u k j y p v
>>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>#7 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#8 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#9 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#10 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#11 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#12 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>
>>>>>>>>>>>>#$group_c
>>>>>>>>>>>>
>>>>>>>>>>>> # Id M mm x b u k j y p v
>>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>#or if you want it like this:
>>>>>>>>>>>>res2<-split(res,names(res))
>>>>>>>>>>>>
>>>>>>>>>>>>res2[["group_b"]]
>>>>>>>>>>>>
>>>>>>>>>>>>#$group_b
>>>>>>>>>>>># Id M mm x b u k j y p v
>>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>
>>>>>>>>>>>>#$group_b
>>>>>>>>>>>> # Id M mm x b u k j y p v
>>>>>>>>>>>>#1 aAA 1 2 739 0.1257000 2 2 AA 2 8867 8926
>>>>>>>>>>>>#2 aAAAA 1 2 2263 0.0004000 2 2 AR 4 7640 8926
>>>>>>>>>>>>#3 aA 2 1 1 0.0845435 2 AA 2 6790 734,1092 NA
>>>>>>>>>>>>#4 aAA 1 2 1965 0.0007000 4 3 AR 2 11616 8926
>>>>>>>>>>>>#5 aAAA 1 3 3660 0.0008600 18 3 AA 2 20392 496
>>>>>>>>>>>>#6 AA na 2 1972 0.0007000 11 3 AR 25 509 734
>>>>>>>>>>>>
>>>>>>>>>>>>Hope this helps.
>>>>>>>>>>>>
>>>>>>>>>>>>A.K.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>----- Original Message -----
>>>>>>>>>>>>From: "veracosta...@gmail.com" <veracosta...@gmail.com>
>>>>>>>>>>>>To: smartpink...@yahoo.com
>>>>>>>>>>>>Cc:
>>>>>>>>>>>>Sent: Friday, February 15, 2013 9:15 AM
>>>>>>>>>>>>Subject: reading data
>>>>>>>>>>>>
>>>>>>>>>>>>Hi,
>>>>>>>>>>>>I post yesterday and you helped me. I have little problem.
>>>>>>>>>>>>
>>>>>>>>>>>>At first, I never worked with regular expressions...
>>>>>>>>>>>>
>>>>>>>>>>>>The code that you gave me it's ok, but my files are inside the
>>>>>>>>>>>>folders a1,a2,a3. I try to explain better.
>>>>>>>>>>>>
>>>>>>>>>>>>I have one folder named "data". Inside this folder I have some
>>>>>>>>>>>>other folders named "a1","a2","b1",b2",...and inside of each one of
>>>>>>>>>>>>that I have some files. I want only the file "mmmmmm.txt" (in all
>>>>>>>>>>>>folders I have One file with this name).
>>>>>>>>>>>>The name of the folder give me the name of the group,but I need to
>>>>>>>>>>>>read the file inside. And after, have "group_a",
>>>>>>>>>>>>group_"b"...because I need to work with this data grouped (and know
>>>>>>>>>>>>the name of the group).
>>>>>>>>>>>>
>>>>>>>>>>>>Thank you.
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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