You can choose from the following predefined functions:
SYMBOL_to_ENTREZID()
, ENTREZID_to_SYMBOL
, SYMBOL_to_ENSEMBL
, ENSEMBL_to_SYMBOL
,
SYMBOL_to_REFSEQ
, REFSEQ_to_SYMBOL
.
library(idconv) SYMBOL_to_ENTREZID(c("EGR1", "FOS")) ENTREZID_to_SYMBOL(c("1958", "2353")) SYMBOL_to_ENSEMBL(c("EGR1", "FOS")) ENSEMBL_to_SYMBOL(c("ENSG00000120738", "ENSG00000170345"))
You can use the generic function to map other identifiers:
IDX_to_IDY(ids = "NM_005252", from = "REFSEQ", to = "ENSEMBL")
Or simply define your own custom conversion function:
REFSEQ_to_ENSEMBL <- function(ids) IDX_to_IDY(ids = ids, from = "REFSEQ", to = "ENSEMBL") REFSEQ_to_ENSEMBL("NM_005252")
If more than one mapping is available, AnnotationDbi
returns a warning (1:many mappings) and
idconv
wrapper functions return concatenated target IDs by default.
If desired, wrapper functions in this package can be forced to return unique mappings.
Forcing unique mappings is however not recommended.
SYMBOL_to_ENSEMBL("IER3", force_unique = F) # default SYMBOL_to_ENSEMBL("IER3", force_unique = NA) SYMBOL_to_ENSEMBL("IER3", force_unique = T)
When converting to RefSeq, a subtype for target IDs can be specified, eg. NM
or NP
:
SYMBOL_to_REFSEQ("IER3", to_sub = "NM") SYMBOL_to_REFSEQ("IER3", to_sub = "NP")
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