MultiAssayExperiment-helpers {MultiAssayExperiment}R Documentation

A group of helper functions for manipulating and cleaning a MultiAssayExperiment

Description

A set of helper functions were created to help clean and manipulate a MultiAssayExperiment object.

Usage

intersectRows(x)

intersectColumns(x)

## S4 method for signature 'MultiAssayExperiment'
duplicated(x, incomparables = FALSE, ...)

mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...)

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

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

longFormat(object, ...)

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

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

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

wideFormat(object, ...)

## S4 method for signature 'MultiAssayExperiment'
wideFormat(object, colDataCols = NULL,
  key = NULL, ...)

## S4 method for signature 'ExperimentList'
wideFormat(object, ...)

## S4 method for signature 'ANY'
wideFormat(object, ...)

Arguments

x

A MultiAssayExperiment

incomparables

unused argument

...

Additional arguments. See details.

replicates

A list of LogicalLists indicating multiple / duplicate entries for each biological unit, see the duplicated output

simplify

A function for merging repeat measurements in experiments as indicated by replicates for MultiAssayExperiment

object

Any supported class object

colDataCols

selected colData columns to include in the output

key

name of column whose values will used as variables in the wide dataset from spread. If none are specified, assay, rowname, and colname will be combined

Details

The mergeReplicates function is a house-keeping method for a MultiAssayExperiment where only complete.cases are returned, replicate measurements are averaged (by default), and columns are aligned by the row order in colData. Additional arguments can be passed on to the simplify function.

The mergeReplicates "ANY" method consolidates duplicate measurements for rectangular data structures, returns object of the same class (endomorphic)

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.

mergeReplicates

The mergeReplicates function makes use of the output from duplicated which will point out the duplicate measurements by biological unit in the MultiAssayExperiment. This function will return a MultiAssayExperiment with merged replicates.

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 colData columns with the colDataCols argument (MultiAssayExperiment method only).

wideFormat

The wideFormat MultiAssayExperiment method returns standardized wide DataFrame where each row represents an observation or biological unit as represented in colData. Optionally, colData columns can be added to the data output. The wideFormat method for an ExperimentList returns a list of wideFormat DataFrames. The "ANY" method returns a wide format DataFrame.


[Package MultiAssayExperiment version 1.4.9 Index]