fig.venn: Venn diagram for p-values

In LXQin/PRECISION.seq: Comparison of Depth Normalization Methods

Description

Venn diagram is used to identify the performance of different normalization methods based on intersection of differential expressed genes.

Usage

fig.venn(truth.DEA.pval, DEA.res.pval, Pvalue, title)

Arguments

truth.DEA.pval	p-values of differential expression analysis results from the benchmark (gold standard) obtained from DE.voom, DE.edge, or any method from the users by storing the results as same as DE methods in the package (including DE genes, p-values and log2 fold changes)
DEA.res.pval	p-values as a result from prior differential expression analysis, e.g. using DE.voom or DE.edgeR.
Pvalue	Cut-off point for p-values for identifying significant differential expression.
title	optional, figure title

Value

A Venn diagram

Examples

benchmark.voom <- DE.voom(RC = data.benchmark, groups = data.group, P = 0.01)
test.voom <- DE.voom(RC = data.test, groups = data.group, P = 0.01)
fig.venn(truth.DEA = benchmark.voom$p.val, DEA.res = test.voom$p.val, Pvalue = 0.01)

LXQin/PRECISION.seq documentation built on Dec. 18, 2021, 3:41 a.m.