try this:
> x <- read.table(textConnection("SampleID A1 A2 A3 A4
+ GM920222 GATTGCC GATTGCC GATAGAC GATAGAC
+ GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
+ GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
+ GM960023 GATTGCC GTCATCA GATTGCC GATTGCC
+ GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
+ GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
+ GM920034 GATTGCC GTCATCA GATTGCA GATTGCA
+ GM920096 GATTGCC GATTGCC GATTGCA GATTGCC
+ GM930029 GTCATCA GATTGCC GTCATCA GATTGCC
+ GM940031 GATTGCC GAGTGCA GATTGCA ACTAGAA
+ GM960028 GATTGCC GAGTGCA GATTGCA ACTAGAA
+ GM980007 GTCATCA GATTGCC ACTTGAA GTCATCA
+ GM970009 ACTAGAA GTCAGAA GTCAGCA ACTAGCA
+ GM930026 ACTAGAA GAGTGCA GAGTGCA ACTAGAA
+ GM920031 GATTGCC GTCATCA GATTGCC GATTGCC
+ GM990105 GATTGCC GATTGCC GTCAGCA GTCAGCA
+ GM920202 GATTGCC GATTGCC GATTGCC GATTGCC
+ GM920089 GAGTGCA GTCAGAA ACTATCA GATTGCC
+ GM980051 ACTAGAA ACTAGAA GATAGCC GATAGCC
+ GM930109 GTCATCA GAGTGCA GTTTTAA ACTAGAA
+ GM940039 GTCATCA GAGTGCA GTTTGCC ACTTTCA
+ GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
+ GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
+ GM030005 ACTAGAA GAGTGCA ACTAGAA ACTAGAA
+ GM050009 ACTAGAA GATTGCC GATTGCC ACTAGAA
+ GM990027 GATTGCC GAGTGCA GATTGCA GATTGCC"), header=TRUE, as.is=TRUE)
> x <- as.matrix(x)
> t(apply(x, 1, function(.row){
+ # separate characters
+ z <- do.call(rbind, strsplit(.row[-1], ''))
+ # combine each column
+ z.col <- t(apply(z, 2, paste, collapse=''))
+ # add the ID
+ cbind(.row[1], z.col)
+ }))
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] "GM920222" "GGGG" "AAAA" "TTTT" "TTAA" "GGGG" "CCAA" "CCCC"
[2,] "GM930040" "GGAG" "TACA" "CGTT" "ATAT" "TGTG" "CCAC" "AAAC"
[3,] "GM930040" "GGAG" "TACA" "CGTT" "ATAT" "TGTG" "CCAC" "AAAC"
[4,] "GM960023" "GGGG" "ATAA" "TCTT" "TATT" "GTGG" "CCCC" "CACC"
[5,] "GM920224" "AGGA" "CTTC" "TCCT" "AAAA" "GTTG" "ACCA" "AAAA"
[6,] "GM920224" "AGGA" "CTTC" "TCCT" "AAAA" "GTTG" "ACCA" "AAAA"
[7,] "GM920034" "GGGG" "ATAA" "TCTT" "TATT" "GTGG" "CCCC" "CAAA"
[8,] "GM920096" "GGGG" "AAAA" "TTTT" "TTTT" "GGGG" "CCCC" "CCAC"
[9,] "GM930029" "GGGG" "TATA" "CTCT" "ATAT" "TGTG" "CCCC" "ACAC"
[10,] "GM940031" "GGGA" "AAAC" "TGTT" "TTTA" "GGGG" "CCCA" "CAAA"
[11,] "GM960028" "GGGA" "AAAC" "TGTT" "TTTA" "GGGG" "CCCA" "CAAA"
[12,] "GM980007" "GGAG" "TACT" "CTTC" "ATTA" "TGGT" "CCAC" "ACAA"
[13,] "GM970009" "AGGA" "CTTC" "TCCT" "AAAA" "GGGG" "AACC" "AAAA"
[14,] "GM930026" "AGGA" "CAAC" "TGGT" "ATTA" "GGGG" "ACCA" "AAAA"
[15,] "GM920031" "GGGG" "ATAA" "TCTT" "TATT" "GTGG" "CCCC" "CACC"
[16,] "GM990105" "GGGG" "AATT" "TTCC" "TTAA" "GGGG" "CCCC" "CCAA"
[17,] "GM920202" "GGGG" "AAAA" "TTTT" "TTTT" "GGGG" "CCCC" "CCCC"
[18,] "GM920089" "GGAG" "ATCA" "GCTT" "TAAT" "GGTG" "CACC" "AAAC"
[19,] "GM980051" "AAGG" "CCAA" "TTTT" "AAAA" "GGGG" "AACC" "AACC"
[20,] "GM930109" "GGGA" "TATC" "CGTT" "ATTA" "TGTG" "CCAA" "AAAA"
[21,] "GM940039" "GGGA" "TATC" "CGTT" "ATTT" "TGGT" "CCCC" "AACA"
[22,] "GM050099" "GGGA" "ATTC" "GCTT" "TAAT" "GGTT" "CACC" "AACA"
[23,] "GM050099" "GGGA" "ATTC" "GCTT" "TAAT" "GGTT" "CACC" "AACA"
[24,] "GM030005" "AGAA" "CACC" "TGTT" "ATAA" "GGGG" "ACAA" "AAAA"
[25,] "GM050009" "AGGA" "CAAC" "TTTT" "ATTA" "GGGG" "ACCA" "ACCA"
[26,] "GM990027" "GGGG" "AAAA" "TGTT" "TTTT" "GGGG" "CCCC" "CAAC"
On Wed, May 19, 2010 at 8:29 AM, Laetitia Schmid <laeti...@gmt.su.se> wrote:
> Dear Wu Gong and Peter Ehlers,
> thank you very much for your help debugging my script.
>
> Now I have a general following up question:
> Is there a straightforward way to rearrange the following dataset so that
> all first letters of each column will be combined in one column, all the
> second letters in a second column, all the third ones in a third column and
> so on, resulting in 7 columns,
> i.e. for the first individual (GM920222) GGGG AAAA TTTT TTAA GGGG CCAA CCCC
> ?
>
> Thank you very much,
> Laetitia
>
> SampleID A1 A2 A3 A4
> GM920222 GATTGCC GATTGCC GATAGAC GATAGAC
> GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
> GM930040 GTCATCA GAGTGCA ACTATAA GATTGCC
> GM960023 GATTGCC GTCATCA GATTGCC GATTGCC
> GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
> GM920224 ACTAGAA GTCATCA GTCATCA ACTAGAA
> GM920034 GATTGCC GTCATCA GATTGCA GATTGCA
> GM920096 GATTGCC GATTGCC GATTGCA GATTGCC
> GM930029 GTCATCA GATTGCC GTCATCA GATTGCC
> GM940031 GATTGCC GAGTGCA GATTGCA ACTAGAA
> GM960028 GATTGCC GAGTGCA GATTGCA ACTAGAA
> GM980007 GTCATCA GATTGCC ACTTGAA GTCATCA
> GM970009 ACTAGAA GTCAGAA GTCAGCA ACTAGCA
> GM930026 ACTAGAA GAGTGCA GAGTGCA ACTAGAA
> GM920031 GATTGCC GTCATCA GATTGCC GATTGCC
> GM990105 GATTGCC GATTGCC GTCAGCA GTCAGCA
> GM920202 GATTGCC GATTGCC GATTGCC GATTGCC
> GM920089 GAGTGCA GTCAGAA ACTATCA GATTGCC
> GM980051 ACTAGAA ACTAGAA GATAGCC GATAGCC
> GM930109 GTCATCA GAGTGCA GTTTTAA ACTAGAA
> GM940039 GTCATCA GAGTGCA GTTTGCC ACTTTCA
> GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
> GM050099 GAGTGCA GTCAGAA GTTATCC ACTTTCA
> GM030005 ACTAGAA GAGTGCA ACTAGAA ACTAGAA
> GM050009 ACTAGAA GATTGCC GATTGCC ACTAGAA
> GM990027 GATTGCC GAGTGCA GATTGCA GATTGCC
> GM990066 GATTGCC GTCATCA GTCATCA GATTGCC
>
> ______________________________________________
> 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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
______________________________________________
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.
