genesName_ENSEMBL: Obtain the genes names in the genomic regions of interest...

In TiphaineCMartin/coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Obtain the genes names in the genomic regions of interest from ENSEMBL

Description

Obtain the genes names in the genomic regions of interest from ENSEMBL

Usage

genesName_ENSEMBL(gen, chr, start, end, dataset)

Arguments

gen	the name of the genome
chr	the chromosome of interest
start	the first position in the region of interest (the smallest value)
end	the last position in the region of interest (the largest value)
dataset	Name of the database to select genes

Details

Can be null

Value

List of name of genes found in this region of interest.

Author(s)

Tiphaine Martin

References

go to ENSEMBL

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()){
  dataset<- "hsapiens_gene_ensembl"
  geneNameEnsembl<- genesName_ENSEMBL(gen,chr,start,end,dataset)
  geneNameEnsembl
} else {
  data(geneNameEnsembl)
  geneNameEnsembl
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.