commonSamples {MultiDataSet} | R Documentation

## Method to select samples that are present in all datasets.

### 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)

[Package MultiDataSet version 1.14.0 Index]