upsetTimeCoverage: Number of detected features per sample

Description Usage Arguments Value Examples

Description

How many proteins/peptides are detected in each sample. Anything else than NA is considered detected.

Usage

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upsetTimeCoverage(x, ...)

## S4 method for signature 'SilacProteinExperiment'
upsetTimeCoverage(
  x,
  assayName,
  conditionCol,
  maxMissing = 0,
  returnList = FALSE,
  ...
)

## S4 method for signature 'SilacPeptideExperiment'
upsetTimeCoverage(
  x,
  assayName,
  maxMissing = 0,
  conditionCol,
  returnList = FALSE,
  ...
)

## S4 method for signature 'SilacProteomicsExperiment'
upsetTimeCoverage(
  x,
  assayName,
  maxMissing = 0,
  conditionCol,
  returnList = FALSE,
  ...
)

Arguments

x

A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.

...

Further arguments passed to upset().

assayName

Name of the assay to use in the plot.

conditionCol

A character, which indicates the column name in colData(x) that defines the different experiment conditions.

maxMissing

A numerical indicating how many timepoints can a protein/peptide miss.

returnList

A logical indicating if the list used for the plot should be returned instead.

Value

A barplot or a data.frame.

Examples

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data('wormsPE')
upsetTimeCoverage(x = ProtExp(wormsPE),
                assayName = 'ratio',
                maxMissing = 2)

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.