orthofinder2 | R Documentation |
Run Orthofinder2 from R.
orthofinder2(
proteome_folder,
use_existing_output = FALSE,
import_type = NULL,
comp_cores = 1,
of_path = NULL
)
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 |
import_type |
type of
|
comp_cores |
number of cores that shall be used for parallel processing. Default is |
of_path |
a character string specifying the path to the locally installed |
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).
Hajk-Georg Drost
## Not run:
# 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)
## End(Not run)
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