filterByMissingTimepoints {pulsedSilac} | R Documentation

## Filter proteins/peptides by the amount of measurements overtime

### Description

Searches for proteins/peptides that are not found in all timepoints. This can be done for each condition independently (strict = FALSE) or shared across conditions (strict = TRUE).

### Usage

    filterByMissingTimepoints(x, ...)

    ## S4 method for signature 'SilacProteinExperiment'
    filterByMissingTimepoints(
      x,
      assayName,
      maxMissing = 0,
      strict = TRUE,
      conditionCol,
      returnVector = FALSE
    )

    ## S4 method for signature 'SilacPeptideExperiment'
    filterByMissingTimepoints(
      x,
      assayName,
      maxMissing = 0,
      strict = TRUE,
      conditionCol,
      returnVector = FALSE
    )

    ## S4 method for signature 'SilacProteomicsExperiment'
    filterByMissingTimepoints(
      x,
      assayName,
      maxMissing = 0,
      strict = TRUE,
      conditionCol,
      returnVector = FALSE
    )

### Arguments

`x` | A `SilacProteinExperiment`, `SilacPeptideExperiment` or a `SilacProteomicsExperiment` object.
`...` | Unused.
`assayName` | A character indicating which assay will be used to count the number of missed timepoints.
`maxMissing` | A numeric indicating how many timepoints are allowed to be missed.
`strict` | Logical: if TRUE, then proteins have to meet the maxMissing criteria in all conditions and time replicates to pass; if FALSE then proteins only have to meet the maxMissing criteria in one condition or time replicate to pass.
`conditionCol` | A `character`, which indicates the column name in colData(x) that defines the different experiment conditions.
`returnVector` | Logical: if TRUE then a vector with the positions to be subset is returned.

### Value

A `SilacProteinExperiment`, `SilacPeptideExperiment` or a `SilacProteomicsExperiment` object or a logical vector with the rows that pass the minimum number of desired timepoints.

### Examples

    data('wormsPE')
    filterByMissingTimepoints(wormsPE,
                              assayName = 'ratio',
                              maxMissing = 2,
                              strict = FALSE)

[Package pulsedSilac version 1.6.0 Index]