Hello, I would like to do something with a matrix: 1) The columns should be compared pairwise. 2) And the result should be a matrix. I try to illustrate the problem with a testset.> mrs1 rs2 rs3 [1,] 1 1 1 [2,] 0 1 0 [3,] 2 0 1> dput (m)structure(c(1, 0, 2, 1, 1, 0, 1, 0, 1), .Dim = c(3L, 3L), .Dimnames = list( NULL, c("rs1", "rs2", "rs3")))> which (m[,1] !=0&m[,2] != 0) #How many rows between two columns that areboth non zero How can I automate the pairwise which-statement? As result I would like to have a matrix like this rs1 rs2 rs3 rs1 rs2 1 rs3 2 1 Is there a tool in R that helps? Thanks Hermann [[alternative HTML version deleted]]
I believe your query is too vague to coherently (and generally) answer, but have a look at ?outer . -- Bert On Wed, May 15, 2013 at 12:57 PM, Hermann Norpois <hnorpois@gmail.com>wrote:> Hello, > > I would like to do something with a matrix: > 1) The columns should be compared pairwise. > 2) And the result should be a matrix. > > I try to illustrate the problem with a testset. > > > m > rs1 rs2 rs3 > [1,] 1 1 1 > [2,] 0 1 0 > [3,] 2 0 1 > > dput (m) > structure(c(1, 0, 2, 1, 1, 0, 1, 0, 1), .Dim = c(3L, 3L), .Dimnames = list( > NULL, c("rs1", "rs2", "rs3"))) > > which (m[,1] !=0&m[,2] != 0) #How many rows between two columns that are > both non zero > > How can I automate the pairwise which-statement? > > As result I would like to have a matrix like this > > rs1 rs2 rs3 > rs1 > rs2 1 > rs3 2 1 > > Is there a tool in R that helps? > > Thanks > Hermann > > [[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. >-- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]]
Hi,
May be this helps:
c1<-combn(seq_len(ncol(m)),2)
?mat1<- matrix(0,ncol=3,nrow=3,dimnames=list(colnames(m),colnames(m)))
vec1<-unlist(lapply(seq_len(ncol(c1)),function(i) {m1<-m[,c1[,i]];
length(which(m1[,1]!=0 & m1[,2]!=0)) }))
mat1[lower.tri(mat1)]<-vec1
?mat1
#??? rs1 rs2 rs3
#rs1?? 0?? 0?? 0
#rs2?? 1?? 0?? 0
#rs3?? 2?? 1?? 0
#Converting to sparseMatrix
library(Matrix)
?mat2<-as(mat1,"sparseMatrix")
#or
mat2<-Matrix(mat1,sparse=TRUE)
3 x 3 sparse Matrix of class "dtCMatrix"
#??? rs1 rs2 rs3
#rs1?? .?? .?? .
#rs2?? 1?? .?? .
#rs3?? 2?? 1?? .
A.K.
----- Original Message -----
From: Hermann Norpois <hnorpois at gmail.com>
To: r-help <r-help at r-project.org>
Cc:
Sent: Wednesday, May 15, 2013 3:57 PM
Subject: [R] matrix - pairwise comparison of columns
Hello,
I would like to do something with a matrix:
1) The columns should be compared pairwise.
2) And the result should be a matrix.
I try to illustrate the problem with a testset.
> m
? ? rs1 rs2 rs3
[1,]? 1? 1? 1
[2,]? 0? 1? 0
[3,]? 2? 0? 1> dput (m)
structure(c(1, 0, 2, 1, 1, 0, 1, 0, 1), .Dim = c(3L, 3L), .Dimnames = list(
? ? NULL, c("rs1", "rs2",
"rs3")))> which (m[,1] !=0&m[,2] != 0) #How many rows between two columns that
are
both non zero
How can I automate the pairwise which-statement?
As result I would like to have a matrix like this
? ? rs1 rs2 rs3
rs1
rs2? 1
rs3? 2? ? 1
Is there a tool in R that helps?
Thanks
Hermann
??? [[alternative HTML version deleted]]
______________________________________________
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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.