Retrieve genes matching gene identifiers
A vector of NCBI IDs, Ensembl IDs or gene symbols.
TRUE to receive results as-is from Gemma, or FALSE to enable
parsing. Raw results usually contain additional fields and flags that are
omitted in the parsed results.
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
The name of a file to save the results to, or NULL to not write
results to a file. If raw == TRUE, the output will be the raw endpoint from the
API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
Whether or not to overwrite if a file exists at the specified filename.
A data table with information about the querried gene(s)
A list if raw = TRUE.
The fields of the output data.table are:
gene.symbol: Symbol for the gene
gene.ensembl: Ensembl ID for the gene
gene.NCBI: NCBI id for the gene
gene.name: Name of the gene
gene.aliases: Gene aliases. Each row includes a vector
gene.MFX.rank: Multifunctionality rank for the gene
taxon.name: Name of the species
taxon.scientific: Scientific name for the taxon
taxon.ID: Internal identifier given to the species by Gemma
taxon.NCBI: NCBI ID of the taxon
taxon.database.name: Underlying database used in Gemma for the taxon
taxon.database.ID: ID of the underlying database used in Gemma for the taxon
get_genes("DYRK1A")
#> gene.symbol gene.ensembl gene.NCBI
#> <char> <char> <int>
#> 1: DYRK1A ENSG00000157540 1859
#> 2: Dyrk1a ENSMUSG00000022897 13548
#> 3: Dyrk1a ENSRNOG00000001662 25255
#> gene.name gene.aliases
#> <char> <list>
#> 1: dual specificity tyrosine phosphorylation regulated kinase 1A DYRK, DY....
#> 2: dual-specificity tyrosine phosphorylation regulated kinase 1a 2310043O....
#> 3: dual specificity tyrosine phosphorylation regulated kinase 1A Dyrk, PSK47
#> gene.MFX.rank taxon.name taxon.scientific taxon.ID taxon.NCBI
#> <num> <char> <char> <int> <int>
#> 1: 0.9658868 human Homo sapiens 1 9606
#> 2: 0.9685388 mouse Mus musculus 2 10090
#> 3: 0.9535178 rat Rattus norvegicus 3 10116
#> taxon.database.name taxon.database.ID
#> <char> <int>
#> 1: hg38 87
#> 2: mm10 81
#> 3: rn6 86
get_genes(c("DYRK1A", "PTEN"))
#> gene.symbol gene.ensembl gene.NCBI
#> <char> <char> <int>
#> 1: DYRK1A ENSG00000157540 1859
#> 2: PTEN ENSG00000171862 5728
#> 3: Dyrk1a ENSMUSG00000022897 13548
#> 4: Pten ENSMUSG00000013663 19211
#> 5: Dyrk1a ENSRNOG00000001662 25255
#> 6: Pten ENSRNOG00000020723 50557
#> gene.name gene.aliases
#> <char> <list>
#> 1: dual specificity tyrosine phosphorylation regulated kinase 1A DYRK, DY....
#> 2: phosphatase and tensin homolog 10q23del....
#> 3: dual-specificity tyrosine phosphorylation regulated kinase 1a 2310043O....
#> 4: phosphatase and tensin homolog 2310035O....
#> 5: dual specificity tyrosine phosphorylation regulated kinase 1A Dyrk, PSK47
#> 6: phosphatase and tensin homolog MMAC1, M....
#> gene.MFX.rank taxon.name taxon.scientific taxon.ID taxon.NCBI
#> <num> <char> <char> <int> <int>
#> 1: 0.9658868 human Homo sapiens 1 9606
#> 2: 0.9971606 human Homo sapiens 1 9606
#> 3: 0.9685388 mouse Mus musculus 2 10090
#> 4: 0.9992364 mouse Mus musculus 2 10090
#> 5: 0.9535178 rat Rattus norvegicus 3 10116
#> 6: 0.9982868 rat Rattus norvegicus 3 10116
#> taxon.database.name taxon.database.ID
#> <char> <int>
#> 1: hg38 87
#> 2: hg38 87
#> 3: mm10 81
#> 4: mm10 81
#> 5: rn6 86
#> 6: rn6 86