README.md

In uhlitz/idconv: Conversion of gene IDs

idconv

idconv is an R package of wrapper functions to convert gene identifiers available from the org.Hs.eg.db or org.Mm.eg.db bioconductor packages.

Installation

# install bioconductor dependencies
source("http://bioconductor.org/biocLite.R")
if(!require(AnnotationDbi)) biocLite("AnnotationDbi")
if(!require(org.Hs.eg.db)) biocLite("org.Hs.eg.db")
if(!require(org.Mm.eg.db)) biocLite("org.Mm.eg.db")

# install idconv
devtools::install_github("uhlitz/idconv")

Examples

Wrapper functions for specific identifiers:

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"))

## 'select()' returned 1:1 mapping between keys and columns

##   EGR1    FOS 
## "1958" "2353"

ENTREZID_to_SYMBOL(c("1958", "2353"))

## 'select()' returned 1:1 mapping between keys and columns

##   1958   2353 
## "EGR1"  "FOS"

SYMBOL_to_ENSEMBL(c("EGR1", "FOS"))

## 'select()' returned 1:1 mapping between keys and columns

##              EGR1               FOS 
## "ENSG00000120738" "ENSG00000170345"

ENSEMBL_to_SYMBOL(c("ENSG00000120738", "ENSG00000170345"))

## 'select()' returned 1:1 mapping between keys and columns

## ENSG00000120738 ENSG00000170345 
##          "EGR1"           "FOS"

Generic function

You can use the generic function to map other identifiers:

IDX_to_IDY(ids = "NM_005252", from = "REFSEQ", to = "ENSEMBL")

## 'select()' returned 1:1 mapping between keys and columns

##         NM_005252 
## "ENSG00000170345"

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")

## 'select()' returned 1:1 mapping between keys and columns

##         NM_005252 
## "ENSG00000170345"

Non-unique mappings

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

## 'select()' returned 1:many mapping between keys and columns

##                                                                                              IER3 
## "ENSG00000137331;ENSG00000237155;ENSG00000235030;ENSG00000227231;ENSG00000230128;ENSG00000206478"

SYMBOL_to_ENSEMBL("IER3", force_unique = NA)

## 'select()' returned 1:many mapping between keys and columns

## IER3 
##   NA

SYMBOL_to_ENSEMBL("IER3", force_unique = T)

## 'select()' returned 1:many mapping between keys and columns

##              IER3 
## "ENSG00000137331"

Subtype IDs

When converting to RefSeq, a subtype for target IDs can be specified, eg. NM or NP:

SYMBOL_to_REFSEQ("IER3", to_sub = "NM")

## 'select()' returned 1:many mapping between keys and columns

##                  IER3 
## "NM_003897;NM_052815"

SYMBOL_to_REFSEQ("IER3", to_sub = "NP")

## 'select()' returned 1:many mapping between keys and columns

##        IER3 
## "NP_003888"

uhlitz/idconv documentation built on May 3, 2019, 2:23 p.m.