upsetTimeCoverage: Number of detected features per sample

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

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

Usage

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

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

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