camlab-bioml / inferorg Goto Github PK

inferorg is an R package to make it easy to find out the organism and gene ID format that a given set of IDs corresponds to. It is ideal for other packages that want to accept a set of gene IDs without requiring a particular format.

To find out the organism and gene ID format, use the inferorg function:

human_mhc_genes <- c("HLA-A", "HLA-B", "HLA-C")
inferorg(human_mhc_genes)

which outputs:

## $organism
## [1] "human"
## 
## $format
## [1] "symbol"
## 
## $confidence_organism
## [1] 1
## 
## $confidence_format
## [1] 1

The confidence scores provide an idea of certainty of the inferred organism and format: they are high only if the IDs map to that gene/format more selectively than any other gene/format, and if most of the IDs map to that gene/format. See the vignette for more details.

The autoconvert function will also convert between formats without having to specify the input format and organism:

autoconvert(c(21354, 21355), to = "symbol")

outputs:

## [1] "Tap1" "Tap2"

To install the development branch, run:

devtools::install_github("camlab-bioml/inferorg")