commonSamples: Method to select samples that are present in all datasets.

In MultiDataSet: Implementation of MultiDataSet and ResultSet

Description

This method subsets the datasets to only contain the samples that are in all datasets. All sets will have the samples in the same order, taking into account that there can be duplicates.

Usage

commonSamples(object, unify.names = FALSE)

Arguments

object	MultiDataSet that will be filtered.
unify.names	Logical indicating if sample names of the sets should be unified.

Details

If unify.names is TRUE, the sample names of the sets will be unified using the id column of phenodata. This option is only possible when there are no duplicated ids.

Value

A new MultiDataSet with only the common samples.

Examples

 
multi <- createMultiDataSet()
eset <- new("ExpressionSet", exprs = matrix(runif(9), ncol = 3))
fData(eset) <- data.frame(chromosome = c("chr1", "chr1", "chr1"), 
                          start = c(1, 5, 10),end = c(4, 6, 14), 
                          stringsAsFactors = FALSE)
sampleNames(eset) <- c("S1", "S2", "S3")
pData(eset) <- data.frame(id = c("S1", "S2", "S3"))
rownames(pData(eset)) <- c("S1", "S2", "S3")
multi <- add_genexp(multi, eset, dataset.name = "g1")
eset <- new("ExpressionSet", exprs = matrix(runif(8), ncol = 2))
fData(eset) <- data.frame(chromosome = c("chr1", "chr1", "chr1", "chr1"), 
                          start = c(1, 14, 25, 104),end = c(11, 16, 28, 115),
                          stringsAsFactors = FALSE)
sampleNames(eset) <- c("S1", "G2")
pData(eset) <- data.frame(id = c("S1", "G2"))
rownames(pData(eset)) <- c("S1", "G2")

multi <- add_genexp(multi, eset, dataset.name="g2")
commonSamples(multi)

MultiDataSet documentation built on Jan. 31, 2021, 2:01 a.m.