merge: Merge

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

Merges two objects of the same class: SilacProteinExperiment, SilacPeptideExperiment or SilacProteomicsExperiment.

Usage

## S4 method for signature 'SilacProteinExperiment,ANY'
merge(x, y, by, by.x = by, by.y = by, all = TRUE, ...)

## S4 method for signature 'SilacPeptideExperiment,ANY'
merge(x, y, by, by.x = by, by.y = by, all = TRUE, ...)

## S4 method for signature 'SilacProteomicsExperiment,ANY'
merge(
  x,
  y,
  by.prot,
  by.prot.x = by.prot,
  by.prot.y = by.prot,
  by.pept,
  by.pept.x = by.pept,
  by.pept.y = by.pept,
  all = TRUE,
  ...
)

Arguments

x	A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.
y	A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.
by, by.x, by.y	A character indicating the columns used for the merging.
all	A logical indicating if all proteins/peptides should be returned or only the intersect.
...	Further parameters passed into base::merge.
by.prot, by.prot.x, by.prot.y	For SilacProteomicsExperiment objects a character indicating the columns used for the merging of the protein level.
by.pept, by.pept.x, by.pept.y	For SilacProteomicsExperiment objects a character indicating the columns used for the merging of the protein level.

Details

This function is designed to be able to merge different samples from different experiments since it is probable that not the exact same proteins are found in both experiments and therefore cbind cannot be used. It uses the merge base function to merge the rowData data frames and merges the assays based on such merge. The colData data.frame are joined.

For a SilacProteomicsExperiment object it gets a bit more complicated since it is possible that some peptides that were assigned to one protein in one experiment are assigned to another one in another experiment. Therefore the linkerDf data.frame is recalculated.

Value

A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.

Examples

data('wormsPE')
merge(wormsPE[1:10, 1:3], wormsPE[3:10, 4:5])

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