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

Description Usage Arguments Value

View source: R/assignment.R

Description

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

Usage

1
2
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 Oct. 3, 2020, 9:04 a.m.