add_Genes: Add gene information

In HiCociety: Inferring Chromatin Interaction Modules from 3C-Based Data

Add gene information

Description

This function adds a column with a list of genes included in each locus to the ModuleSummary data frame of the hic2community function.

Usage

add_Genes(df, speciesObj)

Arguments

df	The ModuleSummary data frame obtained by running hic2community function
speciesObj	Any Txdb package name corresponding

Details

Adding gene list to ModuleSummary data frame obtained from hic2community function.

Value

A data.frame identical to the input, with an additional "Genes" column. Each entry in this column lists the gene(s) that overlap with the corresponding genomic region. If multiple genes are present, they are concatenated with commas.

Author(s)

Sora Yoon, PhD

Examples

modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
package = 'HiCocietyExample')
mycom = readRDS(modulefile)
mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
'TxDb.Mmusculus.UCSC.mm10.knownGene')

HiCociety documentation built on Feb. 16, 2026, 5:10 p.m.