gprofiler2: gconvert – R documentation

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gconvert

Gene ID conversion.

Description

Interface to the g:Profiler tool g:Convert (https://biit.cs.ut.ee/gprofiler/convert) that uses the information in Ensembl databases to handle hundreds of types of identifiers for genes, proteins, transcripts, microarray probesets, etc, for many species, experimental platforms and biological databases. The input is flexible: it accepts a mixed list of IDs and recognises their types automatically. It can also serve as a service to get all genes belonging to a particular functional category.

Usage

gconvert(
  query,
  organism = "hsapiens",
  target = "ENSG",
  numeric_ns = "",
  mthreshold = Inf,
  filter_na = TRUE
)

Arguments

`query`	character vector that can consist of mixed types of gene IDs (proteins, transcripts, microarray IDs, etc), SNP IDs, chromosomal intervals or term IDs.
`organism`	organism name. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.
`target`	target namespace.
`numeric_ns`	namespace to use for fully numeric IDs (list of available namespaces).
`mthreshold`	maximum number of results per initial alias to show. Shows all by default.
`filter_na`	logical indicating whether to filter out results without a corresponding target.

Value

The output is a data.frame which is a table closely corresponding to the web interface output.

The result fields are further described in the vignette.

Author(s)

Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>

Examples

gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")

gprofiler2

Interface to the 'g:Profiler' Toolset

v0.2.0

GPL (>= 2)

Authors