extract_annotation: Protein annotation extraction

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Protein annotation extraction

Description

Extracts annotation columns from a long-format input

Usage

extract_annotation(protein_ids, quant_table, primary_id = "PG.ProteinGroups",
                   annotation_columns = NULL)

Arguments

protein_ids	A vector of protein ids.
quant_table	A long-format input table. The input is typically the same as input to the preprocess function.
primary_id	The column containing protein ids.
annotation_columns	A vector of columns for annotation.

Value

A table of proteins and associated annotation extracted from the input.

Author(s)

Thang V. Pham

References

Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.

See Also

preprocess

Examples

data("spikeins")
extra_names <- iq::extract_annotation(levels(spikeins$PG.ProteinGroups),
                                      spikeins,
                                      annotation_columns = c("PG.Genes", "PG.ProteinNames"))

iq documentation built on March 31, 2023, 11:34 p.m.