mergeSEs {SEtools}R Documentation

mergeSEs

Description

Merges a list of SummarizedExperiment-class.

Usage

mergeSEs(ll, use.assays = NULL, do.scale = TRUE, commonOnly = TRUE,
  colColumns = NULL, addDatasetPrefix = TRUE, defValues = list())

Arguments

ll

A (named) list of SummarizedExperiment-class

use.assays

Names (or indexes) of the assays to use. By default, all common assays are used.

do.scale

A logical vector indicating (globally or for each assay) whether to perform row unit-variance scaling on each dataset before merging (default TRUE).

commonOnly

Logical; whether to restrict to rows present in all datasets (default TRUE).

colColumns

A character vector specifying 'colData' columns to include (if available in at least one of the datasets). If NULL, everything is kept.

addDatasetPrefix

Logical; whether the name of the dataset should be appended to the sample names (default TRUE).

defValues

A list specifying the default values for 'colColumns' when these are absent.

Value

An object of class SummarizedExperiment-class

Examples

data("SE", package="SEtools")
mergeSEs( list( se1=SE[,1:10], se2=SE[,11:20] ) )


[Package SEtools version 1.0.0 Index]