Make a Gene2Symbol object

makeGene2SymbolFromEnsembl(
  organism,
  genomeBuild = NULL,
  release = NULL,
  ignoreVersion = TRUE,
  format = c("makeUnique", "unmodified", "1:1")
)

makeGene2SymbolFromEnsDb(
  object,
  ignoreVersion = TRUE,
  format = c("makeUnique", "unmodified", "1:1")
)

makeGene2SymbolFromGFF(
  file,
  ignoreVersion = TRUE,
  format = c("makeUnique", "unmodified", "1:1")
)

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.
ignoreVersion	`logical(1)`. Ignore identifier (e.g. transcript, gene) versions. When applicable, the identifier containing version numbers will be stored in `txIdVersion` and `geneIdVersion`, and the variants without versions will be stored in `txId`, `txIdNoVersion`, `geneId`, and `geneIdNoVersion`.
format	`character(1)`. Formatting method to apply: `"makeUnique"`: Recommended. Apply `make.unique()` to the `geneName` column. Gene symbols are made unique, while the gene identifiers remain unmodified. `"unmodified"`: Return `geneId` and `geneName` columns unmodified, in long format. `"1:1"`: For gene symbols that map to multiple gene identifiers, select
object	Object.
file	`character(1)`. File path.

Value

Gene2Symbol.

Functions

makeGene2SymbolFromEnsembl: Make a Gene2Symbol object from Ensembl using an AnnotationHub lookup.
makeGene2SymbolFromEnsDb: Make a Gene2Symbol object from an EnsDb object or annotation package.
makeGene2SymbolFromGFF: Make a Gene2Symbol object from a GFF file.

Note

Updated 2021-03-10.

GFF/GTF file

Remote URLs and compressed files are supported.

Examples

## makeGene2SymbolFromEnsembl ====
x <- makeGene2SymbolFromEnsembl(
    organism = "Homo sapiens",
    ignoreVersion = FALSE
)
#> → Making `GRanges` from Ensembl.
#> → Getting `EnsDb` from AnnotationHub 2.22.0 (2020-10-27).
#> ℹ AH89426: Ensembl 103 EnsDb for Homo sapiens.
#> → Making `GRanges` from `EnsDb`.
#>     Organism: Homo sapiens
#>     Genome build: GRCh38
#>     Release: 103
#>     Level: genes
#> → Defining names by `geneId` column in `mcols`.
#> ℹ 3220 non-unique gene symbols detected.
print(x)
#> Gene2Symbol with 67992 rows and 2 columns
#>                                geneId    geneName
#>                           <character> <character>
#> ENSG00000228572.7   ENSG00000228572.7  AL954722.1
#> ENSG00000182378.15 ENSG00000182378.15      PLCXD1
#> ENSG00000226179.6   ENSG00000226179.6   LINC00685
#> ENSG00000281849.3   ENSG00000281849.3  AL732314.6
#> ENSG00000280767.3   ENSG00000280767.3  AL732314.4
#> ...                               ...         ...
#> LRG_584.1                   LRG_584.1   CYP2C19.1
#> LRG_721.1                   LRG_721.1      AKT1.1
#> LRG_741.1                   LRG_741.1     ALMS1.1
#> LRG_763.1                   LRG_763.1       HTT.1
#> LRG_93.1                     LRG_93.1     ORAI1.1

## makeTx2GeneFromEnsDb ====
if ("EnsDb.Hsapiens.v75" %in% rownames(installed.packages())) {
    x <- makeGene2SymbolFromEnsDb("EnsDb.Hsapiens.v75")
    print(x)
}
#> → Making `GRanges` from `EnsDb`.
#>     Organism: Homo sapiens
#>     Genome build: GRCh37
#>     Release: 75
#>     Level: genes
#> → Defining names by `geneId` column in `mcols`.
#> ℹ 3075 non-unique gene symbols detected.
#> Gene2Symbol with 64102 rows and 2 columns
#>                          geneId        geneName
#>                     <character>     <character>
#> ENSG00000228572 ENSG00000228572 LL0YNC03-29C1.1
#> ENSG00000182378 ENSG00000182378          PLCXD1
#> ENSG00000226179 ENSG00000226179       LINC00685
#> ENSG00000185960 ENSG00000185960            SHOX
#> ENSG00000237531 ENSG00000237531   RP11-309M23.1
#> ...                         ...             ...
#> LRG_187                 LRG_187         LRG_187
#> LRG_239                 LRG_239         LRG_239
#> LRG_311                 LRG_311         LRG_311
#> LRG_415                 LRG_415         LRG_415
#> LRG_93                   LRG_93          LRG_93

## makeGene2SymbolFromGFF ====
file <- pasteURL(
    "ftp.ensembl.org",
    "pub",
    "release-102",
    "gtf",
    "homo_sapiens",
    "Homo_sapiens.GRCh38.102.gtf.gz",
    protocol = "ftp"
)
x <- makeGene2SymbolFromGFF(
    file = file,
    ignoreVersion = FALSE
)
#> → Making `GRanges` from GFF file (Homo_sapiens.GRCh38.102.gtf.gz).
#> → Getting GFF metadata for Homo_sapiens.GRCh38.102.gtf.gz.
#> → Importing 104a6592d9a95_Homo_sapiens.GRCh38.102.gtf.gz at /opt/koopa/opt/r/cache/AcidGenomes using rtracklayer::`import()`.
#> → Defining names by `geneId` column in `mcols`.
#> ℹ 67 non-unique gene symbols detected.
print(x)
#> Gene2Symbol with 60675 rows and 2 columns
#>                              geneId    geneName
#>                         <character> <character>
#> ENSG00000223972.5 ENSG00000223972.5     DDX11L1
#> ENSG00000243485.5 ENSG00000243485.5 MIR1302-2HG
#> ENSG00000284332.1 ENSG00000284332.1   MIR1302-2
#> ENSG00000268020.3 ENSG00000268020.3      OR4G4P
#> ENSG00000240361.2 ENSG00000240361.2     OR4G11P
#> ...                             ...         ...
#> ENSG00000276017.1 ENSG00000276017.1  AC007325.1
#> ENSG00000278817.1 ENSG00000278817.1  AC007325.4
#> ENSG00000277196.4 ENSG00000277196.4  AC007325.2
#> ENSG00000278625.1 ENSG00000278625.1       U6.36
#> ENSG00000277374.1 ENSG00000277374.1        U1.5