hack_class: Hack signature classes

In hacksig: A Tidy Framework to Hack Gene Expression Signatures

Hack signature classes

Description

hack_class() is supposed to be used in combination after hack_sig() in order to classify your samples in one of two or more signature classes.

Usage

hack_class(sig_data, cutoff = "original")

Arguments

sig_data

A tibble result of a call to hack_sig().

cutoff

A character specifying which function to use to categorize samples by signature scores. Can be one of: "original" (default), apply the original publication method; if categorization is not expected, the median score is used as a threshold; "mean"/"median", samples will be classified as "low" or "high" with respect to the mean/median signature score, respectively; "tertiles", samples will be classified as "<= T1" (score lower than first tertile), "(T1, T2]" (score between first and second tertiles), "> T2" (score higher than second tertile); "quartiles", samples will be classified as "<= Q1" (score lower than first quartile), "(Q1, Q2]" (score between first and second quartiles), "(Q2, Q3]" (score between second and third quartiles), "> Q3" (score higher than third quartile).

Value

A tibble with the same dimension as sig_data, a column sample_id indicating sample identifiers and one column for each input signature giving signature classes.

See Also

hack_sig()

Examples

library(dplyr)
hack_sig(test_expr, "immune") %>% hack_class()

hacksig documentation built on March 18, 2022, 6:44 p.m.