Overview

The R package gprofiler2 provides an R interface to the g:Profiler tools. There is a vignette/tutorial at: https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html For a comprehensive list of options and output descriptions for all the tools, please see the vignette.

The reference manual is available at CRAN.

How to use

g:GOSt

To use g:GOSt with the default parameters, only an organism name and a genelist are required as parameters. For a list of available organisms and their corresponding ID-s, please see the list of organisms .

library(gprofiler2)
gostres <- gost(query = c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"),
organism = "hsapiens")

# The result is a named list where “result” is a data.frame with the enrichment analysis results
# and “meta” containing a named list with all the metadata for the query.
head(gostres$result)

The package can be used to plot the enrichment results.

p <- gostplot(gostres, capped = FALSE, interactive = FALSE)
p

g:Convert

gconvert enables to map between genes, proteins, microarray probes, common names, various database identifiers, etc, from numerous databases and for many species.

gconvert(query = c("REAC:R-HSA-3928664", "rs17396340", "NLRP1"), organism = "hsapiens",
target="ENSG", mthreshold = Inf, filter_na = TRUE)

Default target = ENSG database is Ensembl ENSG, but gconvert also supports other major naming conventions like Uniprot, RefSeq, Entrez, HUGO, HGNC and many more. In addition, a large variety of microarray platforms like Affymetrix, Illumina and Celera are available.

For a full list of available namespaces, please see the namespaces list

g:Orth

gorth translates gene identifiers between organisms. For example, to convert gene list between mouse (source_organism = mmusculus) and human (target_organism = hsapiens):

gorth(query = c("Klf4", "Sox2", "71950"), source_organism = "mmusculus",
target_organism = "hsapiens", numeric_ns = "ENTREZGENE_ACC")

g:SNPense

gsnpense converts a list of SNP rs-codes (e.g. rs11734132) to chromosomal coordinates, gene names and predicted variant effects. Mapping is only available for variants that overlap with at least one protein coding Ensembl gene.

gsnpense(query = c("rs11734132", "rs4305276", "rs17396340", "rs3184504"))

Installation