check_subject_info: Check subject level information

In szymczak-lab/harmonizeGeneExprData: Harmonization of gene expression data from GEO and ArrayExpress

Check subject level information

Description

Check if subject information is consistent across all samples.

Usage

check_subject_info(pheno, col.id = NULL, cols.subject)

Arguments

pheno	[data.frame] harmonized phenotype data
col.id	[vector(1)] column name with subject identifier (if NULL, the column name ending on "_id" is used)
cols.subject	[vector(n)] column names to be used for check

Examples

# example study
study.id = "GSE67785"

# extract phenotype data from GEO
pheno.original = extract_pheno_data(
  study.id = study.id)

check_subject_info(
  pheno = pheno.original,
  col.id = "patient:ch1",
  cols.subject = "gender:ch1")

szymczak-lab/harmonizeGeneExprData documentation built on Dec. 1, 2022, 9:07 p.m.