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Check Integrity and Outliers of Expression Set

Source: R/check_eset.R
check_eset.Rd

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

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)
#> ℹ Checking for NA values: 0 found
#> ℹ Checking for -Inf values: 0 found
#> ℹ Checking for +Inf values: 0 found