Aggregate sets' quantitative samples

This function aggregates quantitative samples, applying a summarisation function (fun) to sets of samples defined by a colData variable.

For QFeatures objects, the aggregated set colData is added to the global colData using addAssay(). If an aggregated group name already exists as a row name in the global colData, it is reused only when shared colData variables do not contain conflicting values, otherwise an error is thrown. The aggregation of samples should take place after run joining.

Usage

# S4 method for class 'SummarizedExperiment'
aggregateSamples(object, scol, fun = rowRobustSummary, ...)

# S4 method for class 'QFeatures'
aggregateSamples(
  object,
  i,
  scol,
  name = "newAssay",
  fun = rowRobustSummary,
  ...
)

Arguments

object

An instance of class QFeatures or SummarizedExperiment.

scol

A character() naming the colData variable defining how to group samples. When multiple variables are supplied, their values are concatenated with _ to build the grouping variable.

fun

A function used to aggregate the samples. The function should apply its summarization row-wise.

...

Additional parameters passed to fun.

i

A character(1) naming the set that will be aggregated.

name

A character(1) naming the new set.

Value

A QFeatures object with an additional set or a SummarizedExperiment object. The new set/SummarizedExperiment contains three assays the first named assay containing the result of the aggregation, the second named aggsd containing the standard deviation associated with each aggregated data point and the third named aggcounts containing the number of observation used for each aggregated data point.