combine_pd_eset: Combine Phenotype Data and Expression Set

In IOBR: Immune Oncology Biological Research

Combine Phenotype Data and Expression Set

Description

Merges phenotype data with an expression matrix by matching sample IDs. Optionally filters features, applies feature manipulation, and scales expression data before combining.

Usage

combine_pd_eset(
  eset,
  pdata,
  id_pdata = "ID",
  feas = NULL,
  feature_manipulation = TRUE,
  scale = TRUE,
  choose_who_when_duplicate = c("eset", "pdata")
)

Arguments

eset	Expression matrix with genes/features in rows and samples in columns.
pdata	Data frame containing phenotype/clinical data.
id_pdata	Character string specifying the column name in 'pdata' containing sample identifiers. Default is '"ID"'.
feas	Character vector specifying features to include from 'eset'. If 'NULL', all features are used. Default is 'NULL'.
feature_manipulation	Logical indicating whether to apply feature manipulation to filter valid features. Default is 'TRUE'.
scale	Logical indicating whether to scale (standardize) expression data. Default is 'TRUE'.
choose_who_when_duplicate	Character string specifying which data to prefer when duplicate columns exist. Options are '"eset"' or '"pdata"'. Default is '"eset"'.

Value

Data frame combining phenotype data and (transposed) expression data, with samples in rows and features/phenotypes in columns.

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
eset <- matrix(rnorm(1000), nrow = 100, ncol = 10)
rownames(eset) <- paste0("Gene", 1:100)
colnames(eset) <- paste0("Sample", 1:10)
pdata <- data.frame(
  ID = colnames(eset),
  group = rep(c("A", "B"), each = 5),
  age = rnorm(10, 50, 10)
)
result <- combine_pd_eset(eset = eset, pdata = pdata, scale = FALSE)
dim(result)

IOBR documentation built on May 30, 2026, 5:07 p.m.