Make a Gene2Symbol object

makeGene2SymbolFromEnsembl(organism, genomeBuild = NULL,
  release = NULL)

makeGene2SymbolFromEnsDb(object)

makeGene2SymbolFromGFF(file)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

genomeBuild

character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").

release

integer(1). Ensembl release version (e.g. 90). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.

object

Object.

file

character(1). File path.

Value

Gene2Symbol.

GFF/GTF file

Remote URLs and compressed files are supported.

Examples

## makeGene2SymbolFromEnsembl ==== x <- makeGene2SymbolFromEnsembl(organism = "Homo sapiens")
#> Making GRanges from Ensembl.
#> Matching EnsDb from AnnotationHub 2.16.0 (2019-05-02).
#> Using temporary cache /tmp/RtmpRp21Si/BiocFileCache
#> AH69187: Ensembl 96 EnsDb for Homo sapiens #> Run this code to download EnsDb manually: #> > library(AnnotationHub) #> > ah <- AnnotationHub() #> > edb <- ah[["AH69187"]]
#> Making GRanges from EnsDb object.
#> - Organism: Homo sapiens #> - Genome Build: GRCh38 #> - Ensembl Release: 96 #> - Level: genes
#> Defining broadClass using: geneBiotype, geneName, seqnames
#> Arranging by geneID.
#> 65868 genes detected.
#> 3048 non-unique gene symbol(s) detected.
#> Gene2Symbol with 65868 rows and 2 columns #> geneID geneName #> <character> <character> #> ENSG00000000003 ENSG00000000003 TSPAN6 #> ENSG00000000005 ENSG00000000005 TNMD #> ENSG00000000419 ENSG00000000419 DPM1 #> ENSG00000000457 ENSG00000000457 SCYL3 #> ENSG00000000460 ENSG00000000460 C1orf112 #> ... ... ... #> LRG_995 LRG_995 FUBP1.1 #> LRG_996 LRG_996 ERBB3.1 #> LRG_997 LRG_997 ROS1.1 #> LRG_998 LRG_998 CCND3.1 #> LRG_999 LRG_999 CIC.1
## makeTx2GeneFromEnsDb ==== x <- makeGene2SymbolFromEnsDb("EnsDb.Hsapiens.v75")
#> Making GRanges from EnsDb object.
#> Loading required namespace: EnsDb.Hsapiens.v75
#> - Organism: Homo sapiens #> - Genome Build: GRCh37 #> - Ensembl Release: 75 #> - Level: genes
#> Defining broadClass using: geneBiotype, geneName, seqnames
#> Arranging by geneID.
#> 64102 genes detected.
#> 3075 non-unique gene symbol(s) detected.
#> Gene2Symbol with 64102 rows and 2 columns #> geneID geneName #> <character> <character> #> ENSG00000000003 ENSG00000000003 TSPAN6 #> ENSG00000000005 ENSG00000000005 TNMD #> ENSG00000000419 ENSG00000000419 DPM1 #> ENSG00000000457 ENSG00000000457 SCYL3 #> ENSG00000000460 ENSG00000000460 C1orf112 #> ... ... ... #> LRG_94 LRG_94 LRG_94 #> LRG_96 LRG_96 LRG_96 #> LRG_97 LRG_97 LRG_97 #> LRG_98 LRG_98 LRG_98 #> LRG_99 LRG_99 LRG_99
## makeGene2SymbolFromGFF ==== ## GTF file <- file.path(basejumpTestsURL, "example.gtf") x <- makeGene2SymbolFromGFF(file)
#> Making GRanges from GFF file.
#> Importing example.gtf using rtracklayer::import().
#> Ensembl GTF detected.
#> Defining broadClass using: geneBiotype, geneName, seqnames
#> Arranging by geneID.
#> 17 genes detected.
#> Gene2Symbol with 17 rows and 2 columns #> geneID geneName #> <character> <character> #> ENSMUSG00000025900 ENSMUSG00000025900 Rp1 #> ENSMUSG00000051951 ENSMUSG00000051951 Xkr4 #> ENSMUSG00000064842 ENSMUSG00000064842 Gm26206 #> ENSMUSG00000088333 ENSMUSG00000088333 Gm27396 #> ENSMUSG00000089699 ENSMUSG00000089699 Gm1992 #> ... ... ... #> ENSMUSG00000103147 ENSMUSG00000103147 Gm7341 #> ENSMUSG00000103161 ENSMUSG00000103161 Gm38148 #> ENSMUSG00000103201 ENSMUSG00000103201 Gm37329 #> ENSMUSG00000103377 ENSMUSG00000103377 Gm37180 #> ENSMUSG00000104017 ENSMUSG00000104017 Gm37363
## GFF3 file <- file.path(basejumpTestsURL, "example.gff3") x <- makeGene2SymbolFromGFF(file)
#> Making GRanges from GFF file.
#> Importing example.gff3 using rtracklayer::import().
#> Ensembl GFF3 detected.
#> Defining broadClass using: geneBiotype, geneName, seqnames
#> Arranging by geneID.
#> 20 genes detected.
#> Gene2Symbol with 20 rows and 2 columns #> geneID geneName #> <character> <character> #> ENSMUSG00000025900 ENSMUSG00000025900 Rp1 #> ENSMUSG00000025902 ENSMUSG00000025902 Sox17 #> ENSMUSG00000051951 ENSMUSG00000051951 Xkr4 #> ENSMUSG00000064842 ENSMUSG00000064842 Gm26206 #> ENSMUSG00000088333 ENSMUSG00000088333 Gm27396 #> ... ... ... #> ENSMUSG00000103161 ENSMUSG00000103161 Gm38148 #> ENSMUSG00000103201 ENSMUSG00000103201 Gm37329 #> ENSMUSG00000103377 ENSMUSG00000103377 Gm37180 #> ENSMUSG00000104017 ENSMUSG00000104017 Gm37363 #> ENSMUSG00000104123 ENSMUSG00000104123 Gm37483