Is there any way of subsetting a snp.matrix on just one column, and ending up with a snp.matrix object (rather than a snp object)? Put another way, is there a way of coercing a snp object to be a snp.matrix object? The following example might illustrate the sort of thing I'm trying to do: > library(snpMatrix) > data(testdata) > subsets <- list("none" = NULL, "one" = 1, "two" = 1:2) > sapply(subsets, function(x) class(Autosomes[,x])) none one two "snp.matrix" "snp" "snp.matrix" I couldn't find anything in the documentation, and am struggling figuring out how to do this by coercing to a regular matrix and then back. Thanks Richard -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204

use the old chestnut [,1,drop=FALSE] --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 4 Jun 2008, Richard Pearson wrote: > Is there any way of subsetting a snp.matrix on just one column, and ending up with a snp.matrix object (rather than a snp object)? Put another way, is there a way of coercing a snp object to be a snp.matrix object? The following example might illustrate the sort of thing I'm trying to do: > > > library(snpMatrix) > > data(testdata) > > subsets <- list("none" = NULL, "one" = 1, "two" = 1:2) > > sapply(subsets, function(x) class(Autosomes[,x])) > none one two > "snp.matrix" "snp" "snp.matrix" > > I couldn't find anything in the documentation, and am struggling figuring out how to do this by coercing to a regular matrix and then back. > > Thanks > > Richard > > -- > Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk > School of Computer Science, http://www.cs.man.ac.uk/~pearsonr > University of Manchester, Tel: +44 161 275 6178 > Oxford Road, Mob: +44 7971 221181 > Manchester M13 9PL, UK. Fax: +44 161 275 6204 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > The information transmitted in this electronic communica...{{dropped:10}}

I had done something daft when trying to convert to a regular matrix and back, but have now figured out how to do this - apologies for the noise! For the record here's what I did: subsetSnpMatrix <- function(snpmat, subsetColumns) { new("snp.matrix", matrix( as(snpmat[,subsetColumns], "matrix"), nrow = dim(snpmat)[1], dimnames = list( dimnames(snpmat)[[1]], dimnames(snpmat)[[2]][subsetColumns] ) ) ) } sapply(subsets, function(x) class(subsetSnpMatrix(Autosomes, x))) none one two "snp.matrix" "snp.matrix" "snp.matrix" If anyone has a more elegant solution that doesn't involve coercing to a regular matrix I'd still find it useful. Best wishes Richard. Richard Pearson wrote: > Is there any way of subsetting a snp.matrix on just one column, and > ending up with a snp.matrix object (rather than a snp object)? Put > another way, is there a way of coercing a snp object to be a snp.matrix > object? The following example might illustrate the sort of thing I'm > trying to do: > >> library(snpMatrix) >> data(testdata) >> subsets <- list("none" = NULL, "one" = 1, "two" = 1:2) >> sapply(subsets, function(x) class(Autosomes[,x])) > none one two "snp.matrix" "snp" > "snp.matrix" > I couldn't find anything in the documentation, and am struggling > figuring out how to do this by coercing to a regular matrix and then back. > > Thanks > > Richard > -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204