Convert gene identifiers
convertGeneIdentifiers(
genes,
annotation = "Homo sapiens",
key = "ENSEMBL",
target = "SYMBOL",
ignoreDuplicatedTargets = TRUE
)Character: genes to be converted
OrgDb with genome wide annotation for an organism or
character with species name to query OrgDb, e.g.
"Homo sapiens"
Character: type of identifier used, e.g. ENSEMBL; read
?AnnotationDbi::columns
Character: type of identifier to convert to; read
?AnnotationDbi::columns
Boolean: if TRUE, identifiers that
share targets with other identifiers will not be converted
Character vector of the respective targets of gene identifiers. The
previous identifiers remain other identifiers have the same target (in case
ignoreDuplicatedTargets = TRUE) or if no target was found.
genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510",
"ENSG00000051180")
convertGeneIdentifiers(genes)
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
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#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: Biobase
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#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
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#> findMatches
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#> ENSG00000012048 ENSG00000083093 ENSG00000141510 ENSG00000051180
#> "BRCA1" "PALB2" "TP53" "RAD51"
convertGeneIdentifiers(genes, key="ENSEMBL", target="UNIPROT")
#> loading from cache
#> ENSG00000012048
#> "A0A386INP3/A0A386IPK6/A0A2R8Y7V5/G8I0D8/E9PFZ0/O15129/P38398/Q1RMC1/Q3LRJ0/Q3LRJ6/Q6IN79/Q7KYU9/H0Y850/E7EQW4/A0A9Y1VUM8/E7ENB7/E9PH68/A0A9Y1QQD3/A0A0U1RRA9/H0Y8D8/A0A9Y1QQJ6/A0A386IN41/A0A9Y1QQK3/A0A9Y1QQK7/A0A386IN52/A0A9Y1QPY6/A0A9Y1VR53/C9IZW4/A0A9Y1QQK5/A0A9Y1QQL7/A0A9Y1VVE2/E7EUM2/A0A9Y1VVF5/A0A9Y1VVD0/H0Y8B8/A0A9Y1QPR4/A0A9Y1QQF1/A0A2R8Y587/A0A9Y1QPT7/B4DES0/A0A9Y1QQ47/A0A9Y1QPQ7/A0A9Y1QQ02/A0A9Y1VVF6/A0A9Y1QQ22"
#> ENSG00000083093
#> "A0AA52I2C1/A0A8V8TKZ4/A0A386NC12/I3L1Z5/B4DR89/H3BN63/I3L3R6/A0A8V8TMC9/A0A8V8TMK8/A0A8V8TLC8/A6NIE1/Q86YC2/Q8N7Y6/Q8ND31/Q9H6W1"
#> ENSG00000141510
#> "A0A386NC20/A0A386NC22/A0A386NC55/A0A386NC62/A0A386NCA6/A0A386NCB1/A0A386NCU2/A0A386NCW8/A0A386NCX4/A0A386NDA8/A0A386NDB3/A0A386NFX3/A0A386NFY2/A0A386NG45/K7PPA8/K7PPU4/P04637/Q15086/Q15087/Q15088/Q16535/Q16807/Q16808/Q16809/Q16810/Q16811/Q16848/Q2XN98/Q3LRW1/Q3LRW2/Q3LRW3/Q3LRW4/Q3LRW5/Q86UG1/Q8J016/Q99659/Q9BTM4/Q9HAQ8/Q9NP68/Q9NPJ2/Q9NZD0/Q9UBI2/Q9UQ61/A0A223PQI5/J3KP33/E9PFT5/E7ESS1/H2EHT1/A0A087X1Q1/A0A087WXZ1/A0A087WT22"
#> ENSG00000051180
#> "Q5U0A5/Q06609/B0FXP0/B2R8T6/Q6FHX9/Q6ZNA8/Q9BV60"
# Explicit species name to automatically look for its OrgDb database
sp <- "Homo sapiens"
genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510",
"ENSG00000051180")
convertGeneIdentifiers(genes, sp)
#> loading from cache
#> ENSG00000012048 ENSG00000083093 ENSG00000141510 ENSG00000051180
#> "BRCA1" "PALB2" "TP53" "RAD51"
# Alternatively, set the annotation database directly
ah <- AnnotationHub::AnnotationHub()
sp <- AnnotationHub::query(ah, c("OrgDb", "Homo sapiens"))[[1]]
#> loading from cache
columns(sp) # these attributes can be used to change the attributes
#> [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
#> [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
#> [11] "GENETYPE" "GO" "GOALL" "IPI" "MAP"
#> [16] "OMIM" "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM"
#> [21] "PMID" "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG"
#> [26] "UNIPROT"
convertGeneIdentifiers(genes, sp)
#> ENSG00000012048 ENSG00000083093 ENSG00000141510 ENSG00000051180
#> "BRCA1" "PALB2" "TP53" "RAD51"