check_eset: check_eset - Check integrity and outliers of expression set

In IOBR/IOBR: Immune Oncology Biological Research

check_eset - Check integrity and outliers of expression set

Description

This function is used to check the integrity and outliers of the given expression set, providing corresponding warnings and print results. It detects the presence of missing values, infinite values, and features with zero standard deviation.

Usage

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

Arguments

eset	The matrix to be checked.
print_result	Whether to print the check results. Default is FALSE. If set to TRUE, it will print the results of each check.
estimate_sd	Whether to estimate the standard deviation. Default is FALSE. If set to TRUE, it will estimate the standard deviation for each feature and provide warnings and print results accordingly.

Author(s)

Dongqiang Zeng

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data("eset_stad", package = "IOBR")
# transform count data to tpm
eset <- count2tpm(eset_stad, idType = "ensembl")
check_eset(eset)

IOBR/IOBR documentation built on April 4, 2024, 1:07 a.m.