upsetTimeCoverage {pulsedSilac} | R Documentation

## Number of detected features per sample

### 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)

[Package pulsedSilac version 1.1.4 Index]