gorth: Orthology search.

In egonw/r-gprofiler2: Interface to the 'g:Profiler' Toolset

Description

Interface to the g:Profiler tool g:Orth (https://biit.cs.ut.ee/gprofiler/orth) that, given a target organism, retrieves the genes of the target organism that are similar in sequence to the source organism genes in the input.

Usage

gorth(
  query,
  source_organism = "hsapiens",
  target_organism = "mmusculus",
  numeric_ns = "",
  mthreshold = Inf,
  filter_na = TRUE
)

Arguments

query	vector of gene IDs to be translated.
source_organism	name of the source organism. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.
target_organism	name of the target organism. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.
numeric_ns	namespace to use for fully numeric IDs (list of available namespaces).
mthreshold	maximum number of ortholog names per gene to show.
filter_na	logical indicating whether to filter out results without a corresponding target name.

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 <[e-mail]>, Uku Raudvere <[e-mail]>

Examples

gorth(c("Klf4","Pax5","Sox2","Nanog"), source_organism="mmusculus", target_organism="hsapiens")

egonw/r-gprofiler2 documentation built on Aug. 9, 2020, 12:33 a.m.