geneConverter

The goal of geneConverter is to provides functions to convert gene synonyms to gene names and homologous gene names of several organism includes human.

Installation

You can install the development version of geneConverter like so:

#install.packages("devtools)
library(devtools)
install_github("thekaplanlab/geneConverter")

Example orthoConverter

Here is an example data frame including gene names in one column:

gene_names	Ensembl_ID
aat-1	WBGene00000003
bicd-1	WBGene00016611
gtl-2	WBGene00001795
CG12320	FBgn0038590

orthoConverter function converts gene synonyms (if any) in the selected column to gene names. This makes it easier to transform gene synonyms to gene names even when the column contains a mixture of gene synonyms and gene names. This function can also be used to be sure all elements are gene names and there is no gene synonym in the table. Output is the same data table with all other columns preserved. If given data completely consisist of Ensembl ID’s, please choose Ensembl version of that organism while using ctype argument. If you want there is a table which explains the abbreviation and creatures for ctype argument. You can examine it with View(cre_table).

Usage orthoConverter

df<-orthoConverter(example, "gene_names", ctype = celeg)

converted_genes	Ensembl_ID
SLC7A6	WBGene00000003
SLC7A7	WBGene00000003
SLC7A10	WBGene00000003
SLC7A5	WBGene00000003
SLC7A8	WBGene00000003
BICD1	WBGene00016611
BICD2	WBGene00016611
CG12320	FBgn0038590
TRPM1	WBGene00001795
TRPM3	WBGene00001795
TRPM7	WBGene00001795

If drop = TRUE argument used, result will be like this:

df<-orthoConverter(example, "gene_names", ctype = celeg, drop = TRUE)

	converted_genes	Ensembl_ID
1	SLC7A6	WBGene00000003
2	SLC7A7	WBGene00000003
3	SLC7A10	WBGene00000003
4	SLC7A5	WBGene00000003
5	SLC7A8	WBGene00000003
6	BICD1	WBGene00016611
7	BICD2	WBGene00016611
9	TRPM1	WBGene00001795
10	TRPM3	WBGene00001795
11	TRPM7	WBGene00001795