geneModels: Load gene models

In awuster/geneAttribution: Identification of candidate genes associated with genetic variation

Description

Get gene models as a GenomicRanges object, with gene names in the symbol column For hg19, you may want to use TxDb.Hsapiens.UCSC.hg19.knownGene and for GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene (set as default)

Usage

  geneModels(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene,
  maxGeneLength = 1e+06, genesToInclude, genesToExclude)

Arguments

txdb	GenomicFeatures TxDb object containing genomic coordinates of genes
maxGeneLength	An integer. Gene models that are longer than this are excluded. Optional
genesToInclude	A character vector of gene symbols of genes to include (e.g. only protein coding genes). Optional
genesToExclude	A character vector of gene symbols of genes to exclude. Optional

Value

A GenomicRanges object containing human gene models

Examples

geneModels()
geneModels(genesToInclude = c("CYYR1", "ADAMTS1", "ADAMTS5", "N6AMT1", "LTN1"))

awuster/geneAttribution documentation built on May 11, 2019, 4:11 p.m.