get.soma: Load Raw SomaLogic Proteomic Data From Text File

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

Description

This is the function to read and process raw text file proteomics data from SomaLogic. Data can provided with a label to preserve mapping from SeqId to UniProt Full Name. Study ID is preserved in the ID data column.

Usage

get.soma(path, labels = NULL, id = "SampleId")

Arguments

path	File path to the SomaLogic text file with protein data.
labels	Output of get.labels() function protein mapping dictionary
id	Variable name of Study Identifier in SomaLogic Text File used to map study subjects to clinical data.

Value

Tibble containing raw proteomic data for all measured subjects. Tibble will be labelled if labelling dictionary is provided. Sample ID to map to subject study id is stored in the id variable.

Examples

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

soma.data.fifth <- get.soma('data/somaV5.txt', labels = labels)
soma.data.third <- get.soma('data/somaV3.txt', labels = labels)

## End(Not run)

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