check_eset: Check Integrity and Outliers of Expression Set

In IOBR: Immune Oncology Biological Research

Check Integrity and Outliers of Expression Set

Description

Performs quality checks on an expression matrix to identify missing values, infinite values, and features with zero variance. Issues warnings when potential problems are detected that may affect downstream analyses.

Usage

check_eset(eset, print_result = FALSE, estimate_sd = FALSE)

Arguments

eset	Expression matrix or data frame with genes/features in rows and samples in columns.
print_result	Logical indicating whether to print detailed check results to the console. Default is 'FALSE'.
estimate_sd	Logical indicating whether to check for features with zero standard deviation. Default is 'FALSE'.

Value

Invisibly returns 'NULL'. Function is called for its side effects (printing messages and issuing warnings).

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)
check_eset(eset, print_result = TRUE)

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