moduleAnno: module annotation

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

annotate modules using differentially expressed genes

Usage

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

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.