QFeatures-accessors: List of metacell tags

In samWieczorek/DAPAR2: Tools for the Differential Analysis of Proteins Abundance with R

List of metacell tags

Description

This function gives the list of metacell tags available.

• onlyPresent: In this case, the function gives the tags found in a dataset. In addition, and w.r.t to the hierarchy of tags, if all leaves of a node are present, then the tag corresponding to this node is added.

These names are common to all assays contained in the object. This is why they are stored in the global metadata. This function is used whenever it i s necessary to (re)detect MEC and POV (new dataset or when post processing protein qMetacell after aggregation)

Usage

## S4 method for signature 'QFeatures'
GetMetacellTags(object, i, ...)

## S4 method for signature 'SummarizedExperiment'
GetMetacellTags(object, ...)

## S4 method for signature 'QFeatures'
qMetacell(object, i)

## S4 method for signature 'SummarizedExperiment'
qMetacell(object)

qMetacell(object, i, slotName = "qMetacell") <- value

## S4 method for signature 'QFeatures'
GetUniqueTags(object, i)

## S4 method for signature 'SummarizedExperiment'
GetUniqueTags(object)

.GetMetadataSlot(object, slotName = NULL)

.GetRowdataSlot(object, slotName = NULL)

## S4 method for signature 'QFeatures'
ConnectedComp(object, i, slotName = "ConnectedComp")

## S4 method for signature 'SummarizedExperiment'
ConnectedComp(object, slotName = "ConnectedComp")

ConnectedComp(object, i, slotName = "ConnectedComp") <- value

## S4 method for signature 'QFeatures'
typeDataset(object, i, slotName = "typeDataset")

## S4 method for signature 'SummarizedExperiment'
typeDataset(object, slotName = "typeDataset")

typeDataset(object, i, slotName = "typeDataset") <- value

## S4 method for signature 'QFeatures'
idcol(object, i, slotName = "idcol")

## S4 method for signature 'SummarizedExperiment'
idcol(object, slotName = "idcol")

idcol(object, i, slotName = "idcol") <- value

## S4 method for signature 'QFeatures'
parentProtId(object, i, slotName = "parentProtId")

## S4 method for signature 'SummarizedExperiment'
parentProtId(object, slotName = "parentProtId")

parentProtId(object, i, slotName = "parentProtId") <- value

## S4 method for signature 'QFeatures'
analysis(object, i, slotName = "analysis")

## S4 method for signature 'SummarizedExperiment'
analysis(object, slotName = "analysis")

analysis(object, i, slotName = "analysis") <- value

## S4 method for signature 'QFeatures'
version(object, slotName = "version")

version(object, slotName = "version") <- value

## S4 method for signature 'QFeatures'
design.qf(object, slotName = "design")

design.qf(object, slotName = "design") <- value

mainAssay(object)

## S4 method for signature 'QFeatures'
params(object, i, slotName = "params")

## S4 method for signature 'SummarizedExperiment'
params(object, slotName = "params")

params(object, i, slotName = "params") <- value

## S4 method for signature 'QFeatures'
names_metacell(object, i, slotName = "names_metacell")

## S4 method for signature 'SummarizedExperiment'
names_metacell(object, slotName = "names_metacell")

names_metacell(object, i, slotName = "names_metacell") <- value

Arguments

object	An instance of class SummarizedExperiment or QFeatures.
i	The index or name of the assays to extract the quantitative metadata from. All must have a rowdata variable named as slotName
...	xxx
slotName	xxx
value	xxx

Details

Additional slots for rowdata of a SummarizedExperiment object:

• qMetacell: xxx

Additional slots for Metadata for a QFeatures object:

• xxx: xxxx

Additional slots for Metadata for a SummarizedExperiment object:

• qMetacell: xxxx

• parentProtId: xxx

• idcol: xxxx

• typeDataset: xxx

Value

A vector of tags..

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Quantitative metadata

Default slotName is "qMetacell". The value is an adjacency matrix with row and column names. The matrix will be coerced to compressed, column-oriented sparse matrix (class dgCMatrix) as defined in the Matrix package, as generaled by the sparseMatrix() constructor.

Author(s)

Samuel Wieczorek

Examples

data(Exp1_R25_pept, package="DaparToolshedData")
obj <- Exp1_R25_pept
GetMetacellTags(obj, 1, level="peptide")
GetMetacellTags(obj, 1, level="peptide", onlyPresent=TRUE)

data(ft, package='DaparToolshed')
design.qf(ft)

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