get.Known.Gene.List: get.Known.Gene.List
In favorov/differential.coverage: Differential Coverage package

refer to a known gene list for the annotation functions corrently, we have: gencode hs 19 (current for hg 19), gencode hs 26, gencode hs 28, gencode hs 29, gencode hs 32 (current for hg38), gencode hs 34; ucsc hg 18; uscs hg 19; ucsc hg 38 (all in single-strand option)

1	get.Known.Gene.List(genome.annotation.id = "gencode34")

genome.annotation.id

says what annotation is used to prepare the output. gencode19 (default), gencode29, gencode29 and gencode26 load genes for gencode stable annotations (19 and 29) and for 26 (gencode 19 is for human genome 19, gencode 26, 28 and 29 are for 38 version). hg18, hg19, and hg38 load TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene and TxDb.Hsapiens.UCSC.hg38.knownGene, correspondingly.

single.strand.genes.only

UCSC annotations contain ~500 pair of same-named genes that exist on both strands.The parameter says whether to exclude them from the gene list to be returned. The default is FALSE that allows these genes to be included.

GRanges object that contains the gene annotation. The gene_name metadata field is the gene symbol according to the requested annotation. ucsc* uses org.Hs.eg.db names, the gencode provides its own gene names

favorov/differential.coverage documentation built on Feb. 18, 2022, 5:50 p.m.