DaparToolshed-aggregate: Aggregate an assay's quantitative features
In samWieczorek/Dapar2: Tools for the Differential Analysis of Proteins Abundance with R

DaparToolshed-aggregate

R 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).

xxxxx

Iterative aggregation function

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Quantitative metadata aggregation

xxxxxx xxxx

The function to aggregate the quantitative metadata is

aggQmetadat() xxxxx

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. 12, 2023, 9:54 a.m.