Defunct longFormat method

The longFormat method is defunct and will be removed in the next release. Please use the longForm method instead.

Usage

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

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

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

# S4 method for class '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.

Value

A DataFrame with selected colDataCols, if any.

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.