Utilities {DirichletMultinomial} | R Documentation |
csubset
creates a subset of a count matrix, based on identity
of column phenotypes to a specified value.
csubset(val, x, pheno, cidx = TRUE)
val |
|
x |
A matrix of counts, with rows corresponding to samples and columns to taxonomic groups. |
pheno |
A |
cidx |
A |
A matrix
of counts, with rows satisfying pheno %in%
val
and with columns equal either to ncol(x)
(when
cidx=TRUE
) or the number of columns with non-zero counts after
row subsetting (cidx=FALSE
).
Martin Morgan mailto:mtmorgan@fhcrc.org
## count matrix fl <- system.file(package="DirichletMultinomial", "extdata", "Twins.csv") count <- t(as.matrix(read.csv(fl, row.names=1))) ## phenotype fl <- system.file(package="DirichletMultinomial", "extdata", "TwinStudy.t") pheno0 <- scan(fl) lvls <- c("Lean", "Obese", "Overwt") pheno <- factor(lvls[pheno0 + 1], levels=lvls) names(pheno) <- rownames(count) ## subset dim(count) sum("Lean" == pheno) dim(csubset("Lean", count, pheno)) dim(csubset("Lean", count, pheno, cidx=FALSE))