gogenelist: Generates gene list for selected chromatin interactions

In mworkman13/HiCAGE: Hi-C Annotation and Graphics Ensemble

Description

Generates gene list for selected chromatin interactions

Usage

gogenelist(datafile, proximalmark, distalmark, gene.symbol = FALSE,
  species = "human", bio_mart = "ensembl",
  martset = "hsapiens_gene_ensembl", webhost = "www.ensembl.org",
  geneOnto = TRUE, expression_cutoff = 0)

Arguments

datafile	The GRanges object output from the overlap function
proximalmark	The name of the mark in the GRanges object which you are interested in obtaining nearest gene expression data from
distalmark	The name of the mark in the GRanges object interacting with the proximalmark
gene.symbol	If TRUE, will ouput gene list using official gene symbol. If FALSE, gene list output will use Ensembl ID
bio_mart	BiomaRt used for pulling official gene name
martset	The specific mart or dataset used for gene information
geneOnto	Run gene ontology enrichment using TopGO
gbuild	The genome version of mart to be used
expresscut	Cutoff for expression value in gene list

Value

Returns a gene list sorted by gene expression levels of all genes near the proximal mark that are interacting with the distal mark

Examples

hic_chr20 <- system.file("extdata", "hic_chr20.txt", package = "HiCAGE")
segment_chr20 <- system.file("extdata", "segment_chr20.bed",
    package = "HiCAGE")
rna_chr20 <- system.file("extdata", "rna_chr20.tsv", package = "HiCAGE")
overlapoutput <- overlap(hicfile = hic_chr20,
                         segmentfile = segment_chr20,
                         rnafile = rna_chr20)
gogenelist(datafile = overlapoutput, proximalmark = "PAR",
    distalmark = "EAR")

mworkman13/HiCAGE documentation built on May 23, 2019, 11:58 a.m.