get.labels: Get Protein Names and Labels from SeqId Identifiers

In pranavdorbala/proteomicsHF: ARIC Proteomics of Heart Failure -- Biomarker Discovery Pipeline

Description

This is a function to generate a dictionary to translate from SeqId to Protein Name and Entrez Gene Symbol. Output from this function is used in creating tables, figures, and labels for SeqIds. This function also requires an input for data cleaning flags. Proteins that are flagged will not be included in the final label frame.

Usage

get.labels(path, term, name, gene, flag)

Arguments

path	File Path to SomaLogic Data Dictionary
term	Column Variable ID for the SeqId term
name	Column Variable ID for the UniProt Full Name Column
gene	Column Variable ID for the Entrez Gene Symbol Column
flag	Filtering Function for Proteins that Pass QC

Details

The term, name, gene, and flag functions must be provided as-is (not as strings). This is a quirk of using tidyverse and dplyr.

Value

Tibble with columns term for SeqId, name for UniProt Name, and gene for Entrez Gene Symbol. Data Frame rownames are set as the SeqId identifiers.

Examples

## Not run: 
labels <- get.labels('data/proteinMapping.csv', sid,
                     uniprot.full.name,
                     entrezgenesymbol,
                     flag2 == 0)

## End(Not run)

pranavdorbala/proteomicsHF documentation built on March 9, 2021, 12:22 a.m.