DaparToolshed-aggregate: Aggregate an assay's quantitative features

DaparToolshed-aggregateR Documentation

Aggregate an assay's quantitative features

Description

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 can either be a vector (we then refer to an aggregation by vector) or an adjacency matrix (aggregation by matrix).

The quantitative metadata are aggregated with a function (fun.qmeta).

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

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Usage

## S4 method for signature 'QFeatures'
aggregateFeatures4Prostar(
  object,
  i,
  fcol,
  name = "newAssay",
  fun = MsCoreUtils::robustSummary,
  ...
)

## S4 method for signature 'SummarizedExperiment'
aggregateFeatures4Prostar(
  object,
  fcol,
  fun = MsCoreUtils::robustSummary,
  conds,
  ...
)

aggQmetacell(qMeta, X, level, conds)

aggregateMethods()

Arguments

object

An instance of class QFeatures or SummarizedExperiment

i

The index or name of the assay which features will be aggregated the create the new assay.

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 either a character or a (possibly sparse) matrix. See below for details.

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.

fun

A function used for quantitative feature aggregation. See Details for examples.

...

Additional parameters passed the fun and fun.qmeta.

conds

A character() vector which is the names of conditions for each sample in the dataset.

qMeta

An object of class 'SummarizedExperiment'

X

xxxx

level

A character(1) which is the type of dataset

Details

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Value

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

NA

xxxxx

Iterative aggregation function

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Quantitative metadata aggregation

xxxxxx xxxx

The function to aggregate the quantitative metadata is

  • aggQmetadat() xxxxx

See Also

The QFeatures vignette provides an extended example and the Aggregation vignette, for a complete quantitative proteomics data processing pipeline.

Examples


## ---------------------------------------
## An example QFeatures with PSM-level data
## ---------------------------------------
data(ft, package='DaparToolshed')
ft

## Aggregate peptides into proteins
## using the adjacency matrix
feat1 <- aggregateFeatures4Prostar(object = ft,
i = 1,
name = 'aggregated',
fcol = 'adjacencyMatrix',
fun = colSumsMat,
fun.qmeta = aggQmeta)
feat1

assay(feat1[[1]])
assay(feat1[[2]])
aggcounts(feat1[[2]])
assay(feat1[[3]])
aggcounts(feat1[[3]])
rowData(ft[[2]])
data(ft, package='DaparToolshed')
qMeta <- qMetacell(ft, 1)
X <- adjacencyMatrix(ft, 1)
level <- typeDataset(ft, 1)
conds <- colData(ft)$Condition
aggQmeta <- aggQmetacell(qMeta, X, level, conds)


samWieczorek/DAPAR2 documentation built on Oct. 15, 2023, 1:45 p.m.