extract_geo_characteristics: Extract GEO information

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Extract GEO information

Description

Extracts additional sample information from GEO into separate columns of colData(). Numeric variables are converted from character to numeric and syntactically valid variable names are used for the new columns.

Usage

extract_geo_characteristics(se, cols = NULL)

Arguments

se	RangedSummarizedExperiment-class object
cols	Character or integer. Name or number of column(s) in colData with GEO information (optional, will otherwise be extracted assuming column names contain term 'characteristics').

Value

RangedSummarizedExperiment-class object with GEO information in additional columns in colData()

Examples

library(recount)
data("rse_gene_SRP009615")

rse_gene_SRP009615 = extract_geo_characteristics(se = rse_gene_SRP009615)

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.