check_sig {hacksig}

Check signatures feasibility

Description

check_sig() is a helper function that shows useful information about signatures that you want to test on your gene expression matrix.

Usage

check_sig(expr_data, signatures = "all")

Arguments

expr_data

A normalized gene expression matrix (or data frame) with gene symbols as row names and samples as columns.

signatures

It can be a list of signatures or a character vector indicating keywords for a group of signatures. The default ("all") will cause the function to check for all the signatures implemented in hacksig.

Value

A tibble with a number of rows equal to the number of input signatures and five columns:

• n_genes gives the number of genes composing a signature;

• n_present and frac_present are the number and fraction of genes in a signature which are present in expr_data, respectively;

• missing_genes returns a named list of missing gene symbols for each signature.

See Also

get_sig_info(), hack_sig()

Examples

check_sig(test_expr)
check_sig(test_expr, "estimate")