gprofiler2 (version 0.1.4)

gorth: Orthology search.

Description

Interface to the g:Profiler tool g: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.

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.

Examples

# NOT RUN {
gorth(c("Klf4","Pax5","Sox2","Nanog"), source_organism="mmusculus", target_organism="hsapiens")
# }