subsetBy: Subsetting a MultiAssayExperiment object

In waldronlab/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

Subsetting a MultiAssayExperiment object

Description

A set of functions for extracting and dividing a MultiAssayExperiment

Usage

subsetByRow(x, y, ...)

subsetByColData(x, y)

subsetByColumn(x, y)

subsetByAssay(x, y)

## S4 method for signature 'ExperimentList,ANY'
subsetByRow(x, y, ...)

## S4 method for signature 'ExperimentList,list'
subsetByRow(x, y)

## S4 method for signature 'ExperimentList,List'
subsetByRow(x, y)

## S4 method for signature 'ExperimentList,logical'
subsetByRow(x, y)

## S4 method for signature 'ExperimentList,list'
subsetByColumn(x, y)

## S4 method for signature 'ExperimentList,List'
subsetByColumn(x, y)

## S4 method for signature 'ExperimentList,logical'
subsetByColumn(x, y)

## S4 method for signature 'ExperimentList'
subsetByAssay(x, y)

## S4 method for signature 'MultiAssayExperiment,ANY'
subsetByColData(x, y)

## S4 method for signature 'MultiAssayExperiment,character'
subsetByColData(x, y)

## S4 method for signature 'MultiAssayExperiment,ANY'
subsetByRow(x, y, ...)

## S4 method for signature 'MultiAssayExperiment,ANY'
subsetByColumn(x, y)

## S4 method for signature 'MultiAssayExperiment'
subsetByAssay(x, y)

## S4 method for signature 'MultiAssayExperiment,ANY,ANY,ANY'
x[i, j, k, ..., drop = FALSE]

## S4 method for signature 'MultiAssayExperiment,ANY,ANY'
x[[i, j, ...]]

## S4 replacement method for signature 'MultiAssayExperiment,ANY,ANY'
x[[i, j, ...]] <- value

## S4 replacement method for signature 'MultiAssayExperiment,ANY,ANY,ANY'
x[i, j, ...] <- value

Arguments

x	A MultiAssayExperiment or ExperimentList
y	Any argument used for subsetting, can be a character, logical, integer, list or List vector
...	Additional arguments passed on to lower level functions.
i	Either a character, integer, logical or GRanges object for subsetting by rows
j	Either a character, logical, or numeric vector for subsetting by colData rows. See details for more information.
k	Either a character, logical, or numeric vector for subsetting by assays
drop	logical (default FALSE) whether to drop all empty assay elements in the ExperimentList
value	An assay compatible with the MultiAssayExperiment API

Details

Subsetting a MultiAssayExperiment by the j index can yield a call to either subsetByColData or subsetByColumn. For vector inputs, the subset will be applied to the colData rows. For List-type inputs, the List will be applied to each of the elements in the ExperimentList. The order of the subsetting elements in the List must match that of the ExperimentList in the MultiAssayExperiment.

• subsetBycolData: Select biological units by vector input types

• subsetByColumn: Select observations by assay or for each assay

• subsetByRow: Select rows by assay or for each assay

• subsetByAssay: Select experiments

Value

subsetBy* operations are endomorphic and return either MultiAssayExperiment or ExperimentList depending on the input.

Examples

## Load the example MultiAssayExperiment
example("MultiAssayExperiment")

## Using experiment names
subsetByAssay(mae, "Affy")

## Using numeric indices
subsetByAssay(mae, 1:2)

## Using a logical vector
subsetByAssay(mae, c(TRUE, FALSE, TRUE))

## Subset by character vector (Jack)
subsetByColData(mae, "Jack")

## Subset by numeric index of colData rows (Jack and Bob)
subsetByColData(mae, c(1, 3))

## Subset by logical indicator of colData rows (Jack and Jill)
subsetByColData(mae, c(TRUE, TRUE, FALSE, FALSE))

subsetByColumn(mae, list(Affy = 1:2,
    Methyl450k = c(3,5,2), RNASeqGene = 2:4, GISTIC = 1))

subsetWith <- S4Vectors::mendoapply(`[`, colnames(mae),
    MoreArgs = list(1:2))
subsetByColumn(mae, subsetWith)

## Use a GRanges object to subset rows where ranged data present
egr <- GenomicRanges::GRanges(seqnames = "chr2",
    IRanges::IRanges(start = 11, end = 13), strand = "-")
subsetByRow(mae, egr)

## Use a logical vector (recycling used)
subsetByRow(mae, c(TRUE, FALSE))

## Use a character vector
subsetByRow(mae, "ENST00000355076")

waldronlab/MultiAssayExperiment documentation built on Nov. 4, 2024, 7:51 a.m.