Man pages for philliplab/EpitopeMatcher
Epitope Matcher

BETWEEN10HIV Scoring Matrix 10 for between host evolution
BETWEEN38HIV Scoring Matrix 38 for between host evolution
build_scoring_jobsBuilds scoring jobs from pre-processed inputs
epitope_foundA function that indicates if an epitope was found in the...
find_epitope_in_refFinds the position of the epitope in the reference sequence
flatten_lanl_hlaFlattens the LANL HLA file
get_epitope-methodsReturns the epitope associated with a scoring_job
get_hla_details-methodsReturns the hla details associated with a scoring_job
get_hla_genotype-methodsReturns the hla genotype associated with a scoring_job
get_patient_ids-methodsReturns the ids of the patients in the data structure
get_test_lanl_hla_dataA function that returns a test lanl hla genotype dataset
get_test_patient_hla_dataA function that returns a test patient hla dataset
get_test_query_alignmentA function that returns a test query alignment
LANL_HLA_dataThe class for the data from LANL that describe the HLA...
list_scores_to_computeProcesses the three input files (query_alignment, patient_hla...
match_epitopesComputes similarities between certain epitopes and sequences
match_patient_hla_to_query_alignmentMatches the patient_hla data to the query sequence to check...
Patient_HLAThe class for the data that describes which patients have...
read_lanl_hlaA function that reads a HLA genotype specification file
read_patient_hlaA function that reads a patient HLA genotype specification...
read_query_alignmentReads in the query alignment
run_EpitopeMatcher_appRuns the shiny app for this package
score_all_epitopesGiven a list of scoring jobs, compute the similarities
score_epitopeComputes the similarities between the epitope and the...
Scoring_JobA class that contains all the required information to run an...
WITHIN5HIV Scoring Matrix 5 for within host evolution
philliplab/EpitopeMatcher documentation built on May 25, 2019, 5:05 a.m.