longFormat-deprecated: Deprecated longFormat method

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

Deprecated longFormat method

Description

The longFormat method is deprecated and will be removed in a future release. Please use the longForm method instead.

Usage

longFormat(object, colDataCols = NULL, i = 1L, ...)

## S4 method for signature 'MultiAssayExperiment'
longFormat(object, colDataCols = NULL, i = 1L, ...)

## S4 method for signature 'ANY'
longFormat(object, colDataCols = NULL, i = 1L, ...)

## S4 method for signature 'ExperimentList'
longFormat(object, colDataCols = NULL, i = 1L, ...)

Arguments

object	Any supported class object
colDataCols	A character, logical, or numeric index for colData columns to be included
i	longFormat: The i-th assay in SummarizedExperiment-like objects. A vector input is supported in the case that the SummarizedExperiment object(s) has more than one assay (default 1L), renameColname: Either a numeric or character index indicating the assay whose colnames are to be renamed
...	Additional arguments. See details for more information.

Details

The longFormat "ANY" class method, works with classes such as ExpressionSet and SummarizedExperiment as well as matrix to provide a consistent long and skinny DataFrame.

longFormat

The 'longFormat' method takes data from the ExperimentList in a MultiAssayExperiment and returns a uniform DataFrame. The resulting DataFrame has columns indicating primary, rowname, colname and value. This method can optionally include columns of the MultiAssayExperiment colData named by colDataCols character vector argument. (MultiAssayExperiment method only). The i argument allows the user to specify the assay value for the SummarizedExperiment assay function's i argument.

waldronlab/MultiAssayExperiment documentation built on Jan. 29, 2025, 11:06 a.m.