Interface function to Orthofinder2

Source: R/orthofinder2.R

Run Orthofinder2 from R.

orthofinder2(
  proteome_folder,
  use_existing_output = FALSE,
  import_type = NULL,
  comp_cores = 1,
  of_path = NULL
)

Arguments

proteome_folder

file path to a folder storing the proteome sequences of the species for which orthology inference shall be performed.

use_existing_output

a logical value indicating whether or not an existing Orthofinder2 output folder shall be used fo further import and processing. If use_existing_output = TRUE is selected then please specify the file path to the in proteome_folder where the Orthofinder2 output folder can be found.

import_type

type of Orthofinder2 output that shall be imported after running Orthofinder2. Options are:

  • import_type = "orthogroups_core"

  • import_type = "orthogroups_pairwise"

  • import_type = ""

  • import_type = ""

comp_cores

number of cores that shall be used for parallel processing. Default is cores = 1.

of_path

a character string specifying the path to the locally installed orthofinder executable. A possible specification could be of_path = "/opt/miniconda3/bin/" which internally will translate to /opt/miniconda3/bin/orthofinder. The default is of_path = NULL which means that orthofinder assumes users have their orthofinder executable stored at /opt/miniconda3/bin/orthofinder.

Note

This function assumes that users have OrthoFinder installed via miniconda and stored at ~/opt/miniconda3/bin/. In addition, DIAMOND needs to be installed as executable tool (/usr/local/bin).

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# specify species names
orgs <- c("Arabidopsis lyrata",
          "Capsella rubella", "Solanum lycopersicum")
# download proteome files for all species
biomartr::getProteomeSet(db = "refseq", organisms = orgs, path = "of_proteomes")
# download annotation files for all species
biomartr::getGFFSet(db = "refseq", organisms = orgs, path = "of_gff")
# select longest splice variant per gene locus
retrieve_longest_isoforms_all(proteome_folder = "of_proteomes",
                              annotation_folder = "of_gff",
                              annotation_format = "gff",
                              output_folder = "of_proteomes_longest_sv")
# run orthofinder2 to infer ortho groups for the specified species
orthofinder2(proteome_folder = "of_proteomes_longest_sv", comp_cores = 4)
}