HI,
?list.files()
list.files() #created 4 files in my working directory
#[1] "A_hubs.txt" "A_nonhubs.txt" "B_hubs.txt" "B_nonhubs.txt"
#If you want to do wilcox.test in a pairwise manner:
combn(list.files(),2)
# [,1] [,2] [,3] [,4]
#[1,] "A_hubs.txt" "A_hubs.txt" "A_hubs.txt" "A_nonhubs.txt"
#[2,] "A_nonhubs.txt" "B_hubs.txt" "B_nonhubs.txt" "B_hubs.txt"
# [,5] [,6]
#[1,] "A_nonhubs.txt" "B_hubs.txt"
#[2,] "B_nonhubs.txt" "B_nonhubs.txt"
P_value<-
sapply(as.data.frame(combn(list.files(),2),stringsAsFactors=FALSE),function(x){
x1<-read.table(x[1],sep="",header=TRUE); x2<-
read.table(x[2],sep="",header=TRUE); wilcox.test(x1$TIS_SV,x2$TIS_SV)$p.value})
NAME<-gsub("[.txt]","",apply(as.data.frame(combn(list.files(),2),stringsAsFactors=FALSE),2,
paste,collapse="_"))
res<- data.frame(NAME,P_value,stringsAsFactors=FALSE)
row.names(res)<-1:nrow(res)
res
# NAME P_value
#1 A_hubs_A_nonhubs 0.3684845
#2 A_hubs_B_hubs 0.1388408
#3 A_hubs_B_nonhubs 0.1531984
#4 A_nonhubs_B_hubs 0.7910863
#5 A_nonhubs_B_nonhubs 0.4926012
#6 B_hubs_B_nonhubs 0.6350055
A.K.
----- Original Message -----
From: anupam sinha <anupam.cont...@gmail.com>
To: r-help@r-project.org
Cc:
Sent: Tuesday, September 3, 2013 6:58 AM
Subject: [R] reading files
Dear all,
I need help with some coding. I have a directory with files like these:
A_hubs
A_nonhubs
B_hubs
B_nonhubs
:
:
Each of these files have the following header and content:
GENE TIS_DEG TOT_SV TIS_SV TIS_DISO
ensg1 20 12 4 40
.
.
and so on...
I want to calculate the p-value of the function
wilcox.test(A_hubs$TIS_SV,A_nonhubs$TIS_SV) and store it in a table of the
format
NAME p-value
A 0.05
Can some give me pointers in the direction? Thanks in advance
Anupam
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and provide commented, minimal, self-contained, reproducible code.
