list_scores_to_compute: Processes the three input files (query_alignment, patient_hla...

In philliplab/EpitopeMatcher: Epitope Matcher

Description

First the patient_hla data is matched to the query_alignment match_patient_hla_to_query_alignment, then the lanl_hla file is flattened flatten_lanl_hla, and finally, the jobs are built build_scoring_jobs.

Usage

list_scores_to_compute(query_alignment, patient_hla, lanl_hla)

Arguments

query_alignment	An AAStringSet that contains the multiple sequence alignment of the patient's viral sequences
patient_hla	The data.frame that specifies which query sequence to check against which hla genotypes
lanl_hla	The data.frame (of class LANL_HLA_data) that contains the descriptions of the different HLA genotypes

Details

This list of jobs can then be used to perform the comparisons.

Value

A list of Scoring_Jobs

philliplab/EpitopeMatcher documentation built on Nov. 17, 2020, 3:28 p.m.