infercnv (version 0.8)

get_DE_genes_basic: get_DE_genes_basic

Description

Retrieves genes identified as significantly DE based on the corresponding statistical test as applied to the [e-mail] with tumor/normal comparison

Usage

get_DE_genes_basic(infercnv_obj, p_val_thresh = 0.05, test.use = "wilcoxon")

Arguments

infercnv_obj

infercnv object

p_val_thresh

maximum p-value for defining statistical signficance

test.use

statistical test to use. (default: "t" for t-test)

Value

all_DE_results[[condition_pair]] = list(tumor=tumor_type, normal=normal_type, pvals=pvals, de_genes=genes)