Dear Arun,

Thanks a ton for your help.

Regards,

Anupam


On Tue, Sep 3, 2013 at 7:12 PM, arun <smartpink111@yahoo.com> wrote:

>
>
> 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)$p.value})
>
> NAME<-gsub("[.txt]","",apply(as.data.frame(combn(list.files(),2),stringsAsFactors=FALSE),2,
> paste,collapse="_"))
> res<- data.frame(NAME,P_value,stringsAsFactors=FALSE)
>  row.names(res)<-1:nrow(res)
> res
> #                 NAME   P_value
> #1    A_hubs_A_nonhubs 0.3684845
> #2       A_hubs_B_hubs 0.1388408
> #3    A_hubs_B_nonhubs 0.1531984
> #4    A_nonhubs_B_hubs 0.7910863
> #5 A_nonhubs_B_nonhubs 0.4926012
> #6    B_hubs_B_nonhubs 0.6350055
>
> A.K.
>
>
>
> ----- Original Message -----
> From: anupam sinha <anupam.contact@gmail.com>
> To: r-help@r-project.org
> Cc:
> Sent: Tuesday, September 3, 2013 6:58 AM
> Subject: [R] reading files
>
> Dear all,
>
> I need help with some coding. I have a directory with files like these:
>
> A_hubs
> A_nonhubs
> B_hubs
> B_nonhubs
> :
> :
> Each of these files have the following header and content:
>
> GENE  TIS_DEG   TOT_SV    TIS_SV    TIS_DISO
>
> ensg1   20                 12         4              40
> .
> .
> and so on...
>
> I want to calculate the p-value of the function
> wilcox.test(A_hubs$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
>
>     [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>


-- 
Graduate Student,
Laboratory of Computational Biology,
Center For DNA Fingerprinting And Diagnostics,
4-1-714 to 725/2, Tuljaguda complex
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