filterByMissingTimepoints {pulsedSilac} | R Documentation |
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).
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 )
x |
A |
... |
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 |
returnVector |
Logical: if TRUE then a vector with the positions to be subset is returned. |
A SilacProteinExperiment
, SilacPeptideExperiment
or a
SilacProteomicsExperiment
object or a logical vector with the rows that
pass the minimum number of desired timepoints.
data('wormsPE') filterByMissingTimepoints(wormsPE, assayName = 'ratio', maxMissing = 2, strict = FALSE)