assignment: Assigns a boolean based on a threshold on the likelihood or...

In parklab/SigMA: Signature Multivariate Analysis

Assigns a boolean based on a threshold on the likelihood or mva score for whether the signature is identified

Description

Assigns a boolean based on a threshold on the likelihood or mva score for whether the signature is identified

Usage

assignment(df_in, method = "mva", signame = "Signature_3",
  data = NULL, tumor_type = "breast", do_strict = T, weight_cf)

Arguments

df_in	input data.frame
method	'median_catalog' for likelihood based selection or 'mva' for multivariate analysis score based selection
signame	name of the signature that user wants to identify, 'Signature_3' or 'Signature_msi'
data	'msk', 'seqcap' or 'wgs'
tumor_type	tumor type as listed in https://github.com/parklab/SigMA/ because the thresholds are tumor_type specific
do_strict	sets whether a strict threshold should be applied or a loose one

Value

a data.frame with a single column which contains the boolean indicating the presence of the signature

parklab/SigMA documentation built on Feb. 10, 2024, 6:59 p.m.