RangedRaggedAssay-class {MultiAssayExperiment}R Documentation

An extension of the GRangesList class (DEFUNCT)

Description

An extension of the GRangesList class (DEFUNCT)

Subsetting a RangedRaggedAssay can be done using either rownames and column names

Usage

## S4 method for signature 'RangedRaggedAssay,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'RangedRaggedAssay,GRanges,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'RangedRaggedAssay'
dim(x)

## S4 method for signature 'RangedRaggedAssay'
dimnames(x)

## S4 replacement method for signature 'RangedRaggedAssay,list'
dimnames(x) <- value

## S4 method for signature 'RangedRaggedAssay'
disjoin(x, mcolname = NULL,
  simplify = BiocGenerics::mean, ...)

## S4 method for signature 'RangedRaggedAssay'
show(object)

## S4 method for signature 'RangedRaggedAssay'
longFormat(object, ...)

## S4 method for signature 'RangedRaggedAssay'
mergeReplicates(x, replicates = list(),
  simplify = BiocGenerics::mean, mcolname = NULL, ...)

Arguments

x

A RangedRaggedAssay class

i

Either a character or GRanges class object to subset by rows

j

Either a character, numeric, or logical type for selecting columns (GRangesList method)

...

Additional arguments. See details for more information.

drop

logical (default TRUE) whether to drop empty columns

value

A list object of row and column names

mcolname

A single character string indicating metadata column to use for summaries

simplify

A function for combining duplicate measurements (e.g., mean)

object

A RangedRaggedAssay class object

replicates

mergeReplicates: A list or LogicalList where each element represents a sample and a vector of repeated measurements for that biological unit

Details

The ... argument allows the user to specify arguments in the subsetByOverlaps function. When calling the mergeReplicates method, the additional arguments correspond to those in either the assay method or the mergeReplicates method. The mergeReplicates arguments include a function for applying over the rows (combine) and a vectorized argument which indicates whether the given function is vectorized or not.

Value

A RangedRaggedAssay class object

Methods (by generic)

See Also

findOverlaps-methods

assay,RangedRaggedAssay,missing-method


[Package MultiAssayExperiment version 1.4.9 Index]