In imkeller/immunotation: Tools for working with diverse immune genes

knitr::opts_chunk$set(echo = TRUE)

MHC Restriction Ontology (MRO)

The mro.owl file was downloaded from: http://purl.obolibrary.org/obo/mro.owl immunotation package version 0.99.2 corresponds to MRO OWL version 2021-03-09.

Then the owl format was converted to obo format uding the robot program (http://robot.obolibrary.org/)

robot convert --input ../extdata/mro.owl --format owl --output ../extdata/mro.obo 

Finally, gzip was used to create the file mro.obo.gz, which is located in inst/extdata.

Source files for P groups and G groups

The files hla_nom_g.txt and hla_nom_p.txt were downloaded from the following resource:

wget https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/wmda/hla_nom_g.txt 

wget https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/wmda/hla_nom_p.txt

immunotation package version 0.99.2 corresponds to:

• file: hla_nom_p.txt, date: 2021-04-20
• file: hla_nom_g.txt, date: 2021-04-20

List of valid alleles for AFND query

An optional file AFND_valid_alleles.Rdata is contained in inst/extdata. It is generated by the function update_valid_alleles in the R script AFND_queries.R.

imkeller/immunotation documentation built on Jan. 3, 2023, 1:31 p.m.