annotateProteins: Annotate proteins

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Annotate proteins

Description

annotateProteins adds protein annotations to a proteusData object.

Usage

annotateProteins(pdat, annotation)

Arguments

pdat	A proteusData object containing protein data
annotation	A data frame with a column protein containing protein identifiers, as in pdat$proteins

Details

The only information about proteins proteus package extracts from the evidence file are protein identifiers. These can be in various forms, depending on how MaxQuant was ran. In order to annotate them, two steps are required.

First, the user needs to create a data frame linking protein identifiers (as in pdat$proteins vector) to some metadata. This data frame has to contain a column called protein with the identifiers and any additional columns with annotations, e.g., UniProt IDs, protein names, gene names, domains, GO-terms and so on. These data can be obtained from UniProt. Any annotation columns included will be used by interactive functions plotFID_live and plotVolcano_live.

See fetchFromUniProt for obtaining annotation data from UniProt.

Once the annotation table is created, it can be merged into the proteusData object using annotateProteins function. The order of identifiers in the annotation table is not important. Also, not all proteins have to be present. The merge will add only the matching proteins. As a result, this function returns a proteusData object with annotation field added. It contains an annotation data frame with rows corresponding to the internal list of proteins. This means the rows of this data frame correspond one-to-one to the rows in pdat$tab and pdat$detect, if pdat contains proteins (not peptides).

Value

A proteusData with annotation field added.

Examples

library(proteusLabelFree)
data(proteusLabelFree)

# annotations.id is a data frame with annotations
prodat <- annotateProteins(prodat, annotations.id)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.