moduleAnno: module annotation

Description Usage Arguments Value Examples

View source: R/moduleAnno.R

Description

annotate modules using differentially expressed genes

Usage

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moduleAnno(DEG, background, module.gene, cutoff = 0.05,
  adjust.method = "fdr", prefix = NA, pdf.height = 10,
  pdf.width = 10, sve = FALSE)

Arguments

DEG

a character vector containing up/down regulated genes

background

a charactor vector containing all genes as background in hypergeometric test

module.gene

a data frame containing genes with genome region containing DEH loci from one module, generated from epiNetwork() function. The first column is gene entrez ID, the second column is module lable, the third column is module color

cutoff

Cutoff value of qvalue for gene enrichment (default: 0.05)

adjust.method

one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'(default:fdr)

prefix

a prefix for PDF file name

pdf.height

An integer representing the height (in inches) of the outputted boxplot pdf file (default: 10)

pdf.width

An integer representing the width (in inches) of the outputted boxplot pdf file (default: 10)

sve

A boolean to save the plot (default: FALSE)

Value

a data frame showing modules that were enriched by DEGs and module size, p value and q value

Examples

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data(DEG,package = "epihet")
data(background,package = "epihet")
module<-data.frame(gene=c("NM_000014","NM_000015","NM_000017","NM_000019",
"NM_052960","NR_138250","NM_000037","NM_000038","NM_000039","NM_000044",
"NM_000046","NM_015074","NM_183416","NM_004421","NM_001330311",
"NM_001145210","NM_000097","NM_000103","NM_000104",
"NM_000079","NM_000083","NM_000086","NM_000087","NM_000092","NM_000094",
"NM_000095","NM_006474"),label=rep(c(1,2),c(12,15)),
color=rep(c("purple","brown"),c(12,15)),
stringsAsFactors = FALSE)
module.annotation<-epihet::moduleAnno(DEG$refseq,background$gene,
                                     module.gene=module,
                                     cutoff=0.05,adjust.method = "fdr",
                                     prefix='epipoly',pdf.height = 10,
                                     pdf.width = 10, sve = TRUE)

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.