merge-methods: Merge a subset of the rows or columns of a...
In microbiome/mia: Microbiome analysis

merge-methods

R Documentation

Merge a subset of the rows or columns of a `SummarizedExperiment`

Description

mergeRows/mergeCols merge data on rows or columns of a SummarizedExperiment as defined by a factor alongside the chosen dimension. Metadata from the rowData or colData are retained as defined by archetype.

Usage

mergeRows(x, f, archetype = 1L, ...)

mergeCols(x, f, archetype = 1L, ...)

mergeFeatures(x, f, archetype = 1L, ...)

mergeSamples(x, f, archetype = 1L, ...)

## S4 method for signature 'SummarizedExperiment'
mergeRows(x, f, archetype = 1L, ...)

## S4 method for signature 'SummarizedExperiment'
mergeCols(x, f, archetype = 1L, ...)

## S4 method for signature 'SummarizedExperiment'
mergeFeatures(x, f, archetype = 1L, ...)

## S4 method for signature 'SummarizedExperiment'
mergeSamples(x, f, archetype = 1L, ...)

## S4 method for signature 'TreeSummarizedExperiment'
mergeRows(x, f, archetype = 1L, mergeTree = FALSE, mergeRefSeq = FALSE, ...)

## S4 method for signature 'TreeSummarizedExperiment'
mergeCols(x, f, archetype = 1L, mergeTree = FALSE, ...)

## S4 method for signature 'TreeSummarizedExperiment'
mergeFeatures(
  x,
  f,
  archetype = 1L,
  mergeTree = FALSE,
  mergeRefSeq = FALSE,
  ...
)

## S4 method for signature 'TreeSummarizedExperiment'
mergeSamples(x, f, archetype = 1L, mergeTree = FALSE, ...)

Arguments

`x`	a `SummarizedExperiment` or a `TreeSummarizedExperiment`
`f`	A factor for merging. Must be the same length as `nrow(x)/ncol(x)`. Rows/Cols corresponding to the same level will be merged. If `length(levels(f)) == nrow(x)/ncol(x)`, `x` will be returned unchanged.
`archetype`	Of each level of `f`, which element should be regarded as the archetype and metadata in the columns or rows kept, while merging? This can be single integer value or an integer vector of the same length as `levels(f)`. (Default: `archetype = 1L`, which means the first element encountered per factor level will be kept)
`...`	Optional arguments: Passed on to `sumCountsAcrossFeatures`, with the exception of `subset_row`, `subset_col`
`mergeTree`	`TRUE` or `FALSE`: Should `rowTree()` also be merged? (Default: `mergeTree = FALSE`)
`mergeRefSeq`	`TRUE` or `FALSE`: Should a consensus sequence be calculated? If set to `FALSE`, the result from `archetype` is returned; If set to `TRUE` the result from `DECIPHER::ConsensusSequence` is returned. (Default: `mergeRefSeq = FALSE`)

Details

assay are agglomerated, i.e. summed up. If the assay contains values other than counts or absolute values, this can lead to meaningless values being produced.

These functions are similar to sumCountsAcrossFeatures. However, additional support for TreeSummarizedExperiment was added and science field agnostic names were used. In addition the archetype argument lets the user select how to preserve row or column data.

For merge data of assays the function from scuttle are used.

Value

An object of the same class as x with the specified entries merged into one entry in all relevant components.

Examples

data(esophagus)
esophagus
plot(rowTree(esophagus))
# get a factor for merging
f <- factor(regmatches(rownames(esophagus),
                       regexpr("^[0-9]*_[0-9]*",rownames(esophagus))))
merged <- mergeRows(esophagus,f, mergeTree = TRUE)
plot(rowTree(merged))
#
data(GlobalPatterns)
GlobalPatterns
merged <- mergeCols(GlobalPatterns,colData(GlobalPatterns)$SampleType)
merged

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.