estimate_joint_effects: Wrapper to joint CNA effect estimation using GLMNet

View source: R/logistic_reg_histology.R

estimate_joint_effectsR Documentation

Wrapper to joint CNA effect estimation using GLMNet

Description

Function is still in development

Usage

estimate_joint_effects(cnr, trait, pheno0, pheno1, exclude.cluster = "HC")

Arguments

cnr

a cnr bundle

trait

character, name of the trait of interest to analyze. Must be a column in the phenotype matrix (Y). e.g. "binary1"

pheno0

character, phenotype(s) to use as baseline, e.g. "0"

pheno1

character, phenotype(s) to use as alternate, e.g. "1"

exclude.cluster

character, list of clusters to exclude, e.g. hypersegmented, Stroma, etc. Default "HC"

Value

A CNR object containing joint CNA effect estimates using GLMNet. Analysis is carried out in both 'X' and 'genes' copy number matrices.

Effects are estimated at two Lambda; min, 1se. Lambda values are appended as attributes to the chromInfo, and gene.index, for the bin, respectively.

Examples

data(cnr)

cnr <- estimate_joint_effects(cnr, trait = "binary1", pheno0 = 0, pheno1 = 1)


SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.