Aggregate an assay's quantitative features with shared peptide redistribution

This function aggregates the quantitative features of an assay, applying a summarization function (fun) to sets of features. The fcol variable name points to a rowData column that defines how to group the features during aggregate. This variable has to be an adjacency matrix. This function uses DaparToolshed::inner.aggregate.iter() to aggregate quantitative data.

The list of agregation methods can be obtained with the function aggregateMethods(). This function compiles both methods from the packages DaparToolshed and QFeatures.

Usage

aggregateRedistribution(object, ...)

# S4 method for class 'QFeatures'
aggregateRedistribution(
  object,
  i,
  name = "newAssay",
  fcol,
  init.method = "Mean",
  method = "Mean",
  ponderation = "Global",
  n = NULL,
  uniqueiter = FALSE,
  max_iter = 500
)

# S4 method for class 'SummarizedExperiment'
aggregateRedistribution(
  object,
  fcol,
  init.method = "Mean",
  method = "Mean",
  ponderation = "Global",
  n = NULL,
  uniqueiter = FALSE,
  conds,
  max_iter = 500
)

Arguments

object: An instance of class QFeatures or SummarizedExperiment
...: Additional parameters.
i: The index or name of the assay which features will be aggregated the create the new assay.
name: A character(1) naming the new assay. Default is newAssay. Note that the function will fail if there's already an assay with name.
fcol: A character(1) naming a rowdata variable (of assay i in case of a QFeatures) defining how to aggregate the features of the assay. This variable is a (possibly sparse) matrix. See below for details.
init.method: A function used for initializing the aggregation. Available functions are Sum, Mean, Median, medianPolish or robustSummary. See DaparToolshed::inner.aggregate.iter() for details.
method: A function used for the aggregation. Available functions are Sum, Mean, Median or medianPolish. See DaparToolshed::inner.aggregate.iter() for details.
ponderation: A character(1) defining what to consider to create the coefficient for redistribution of shared peptides. Available values are Global (default), Condition or Sample.
n: A numeric(1) specifying the number of peptides to use for each protein. If NULL, all peptides are considered.
uniqueiter: A boolean indication if there should be only 1 iteration or not.
max_iter: A numeric(1) setting the maximum number of iteration.
conds: A character() vector which is the names of conditions.

Value

A QFeatures object with an additional assay or a SummarizedExperiment object (or subclass thereof).

Details

This function uses DaparToolshed::inner.aggregate.iter() to aggregate quantitative data.

Iterative aggregation function

xxxxxx xxxxx

Quantitative metadata aggregation

The function to aggregate the quantitative metadata is aggQmetadat()

Examples

NULL
#> NULL