gProfileR (version 0.7.0)

gorth: Find orthologs.

Description

Interface to the g:Orth tool. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.

Usage

gorth(query, source_organism = "hsapiens",
  target_organism = "mmusculus", region_query = F, numeric_ns = "",
  mthreshold = Inf, filter_na = T, df = T)

Arguments

query

list of gene IDs to be translated.

source_organism

name of the source organism.

target_organism

name of the target organism.

region_query

interpret query as chromosomal ranges.

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.

df

logical indicating whether the output will be a data.frame or list.

Value

The output can be either a list or a data.frame. The list has an entry for every input gene. The data frame is a table closely corresponding to the web interface output.

Details

To alleviate the problem of having many orthologs per gene (most of them uninformative) one can set a threshold for the number of results. The program tries to find the most informative by selecting the most popular ones.

References

J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler -- a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200

Examples

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