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. intersectRows also works for ExperimentList objects.

• complete.cases: Returns a logical vector corresponding to 'colData' rows that have data across all experiments

• isEmpty: Returns a logical TRUE value for zero length MultiAssayExperiment objects

• intersectRows: Takes all common rows across experiments, excludes experiments with empty rownames

• intersectColumns: A wrapper for complete.cases to return a MultiAssayExperiment with only those biological units that have measurements across all experiments

• replicated: A function that identifies multiple samples that originate from a single biological unit within each assay

• anyReplicated: Displays which assays have replicate measurements

• mergeReplicates: A function that combines replicated / repeated measurements across all experiments and is guided by the replicated return value

• longFormat: A MultiAssayExperiment method that returns a small and skinny DataFrame. The colDataCols arguments allows the user to append colData columns to the data.

• wideFormat: A function to return a wide DataFrame where each row represents an observation. Optional colDataCols can be added when using a MultiAssayExperiment.

• hasRowRanges: A function that identifies ExperimentList elements that have a rowRanges method

• duplicated: (Deprecated) Returns a 'list' of 'LogicalList's that indicate what measurements originate from the same biological unit

Usage

## S4 method for signature 'MultiAssayExperiment'
complete.cases(...)

## S4 method for signature 'MultiAssayExperiment'
isEmpty(x)

intersectRows(x)

intersectColumns(x)

replicated(x)

## S4 method for signature 'MultiAssayExperiment'
replicated(x)

anyReplicated(x)

## S4 method for signature 'MultiAssayExperiment'
anyReplicated(x)

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

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

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

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

wideFormat(object, colDataCols = NULL, check.names = TRUE,
  collapse = "_", i = 1L)

hasRowRanges(x)

## S4 method for signature 'MultiAssayExperiment'
hasRowRanges(x)

## S4 method for signature 'ExperimentList'
hasRowRanges(x)

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

Arguments

Details

The replicated function finds replicate measurements in each assay and returns a list of LogicalLists. Each element in a single LogicalList corresponds to a biological or primary unit as in the sampleMap. Below is a small graphic for one particular biological unit in one assay, where the logical vector corresponds to the number of measurements/samples in the assay:

 >      replicated(MultiAssayExperiment)
 (list str)       '-- $ AssayName
 (LogicalList str)      '-- [[ "Biological Unit" ]]
 Replicated if sum(...) > 1          '-- TRUE TRUE FALSE FALSE

anyReplicated determines if any of the assays have at least one replicate. Note. These methods are not available for the ExperimentList class due to a missing sampleMap structure (by design).

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 ellipsis or ... argument allows the user to provide additional arguments to the simplify functional argument.

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.

The hasRowRanges method identifies assays that support a rowRanges method and return a GRanges object.

Deprecated: For the anyDuplicated and duplicated functions, the incomparables and ellipsis ... arguments are not used. Neither duplicated nor anyDuplicated is supported for ExperimentList due to an unavailable sampleMap.

mergeReplicates

The mergeReplicates function makes use of the output from replicated which will point out the duplicate measurements by biological unit in the MultiAssayExperiment. This function will return a MultiAssayExperiment with merged replicates. Additional arguments can be provided to the simplify argument via the ellipsis (...).

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). The i argument allows the user to specify the assay value in a SummarizedExperiment. It directly relates to the i argument in the assay method.

wideFormat

The wideFormat function returns standardized wide DataFrame where each row represents a biological unit as in the colData. Depending on the data and setup, biological units can be patients, tumors, specimens, etc. Optionally, colData columns can be added to the wide data output (see the colDataCols argument). Metadata columns are generated based on the names produced in the wide format DataFrame. These can be accessed via the mcols function. See the Arguments and longFormat sections for argument descriptions.

hasRowRanges

The hasRowRanges method identifies assays with associated ranged row data by directly testing the method on the object. The result from the test must be a GRanges class object to satisfy the test.