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 1.8.0 Index]