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Get gene homologs between 2 organisms

Source: R/getHomTable.R
getHomTable.Rd

Get gene homologs between 2 organisms

Usage

getHomTable(
  from.org,
  to.org,
  from.source = "Ens_gene",
  to.source = from.source,
  restricted = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  limForCache = 100
)

Arguments

from.org

organism name

to.org

organism name

from.source

the from gene ID database

to.source

the to gene ID database

restricted

boolean indicating if the results should be restricted to current version of to BEID db. If FALSE former BEID are also returned: Depending on history it can take a very long time to return a very large result!

verbose

boolean indicating if the CQL query should be displayed

recache

boolean indicating if the CQL query should be run even if the table is already in cache

filter

character vector on which to filter from IDs. If NULL (default), the result is not filtered: all from IDs are taken into account.

limForCache

if there are more filter than limForCache results are collected for all IDs (beyond provided ids) and cached for futur queries. If not, results are collected only for provided ids and not cached.

Value

a data.frame mapping gene IDs with the following fields:

  • from: the from gene ID

  • to: the to gene ID

See also

getBeIdConvTable

Examples

if (FALSE) { # \dontrun{
getHomTable(
   from.org="human",
   to.org="mouse"
)
} # }