utils: Basic functions of the package

In epitopR: Predict Peptide-MHC Binding

Basic functions of the package

Description

preproc_huII() format and validate allele names

Usage

preproc_huII(allele_in)

pull_seq_huII(alleles_in, tbl_ref_in)

prep_lbl_huII(alleles_in)

comb_pred_tbl(nm_method, nm_sht, nm_fd, thold_score, thold_rank)

find_nonself_huII(dat_in)

pull_ag_self(dat_in)

find_core_mut(dat_in)

Arguments

allele_in	a vector contains allele name(s) pull_seq_huII() pull out sequence of each allele based on ref table
alleles_in	vector, allele names comb_pred_tbl() combine individual prediction tables by method, exclude none-binders and keep strong and weak binders only
tbl_ref_in	dataframe, reference table, default is human_all.csv from github prep_lbl_huII() concatenate allele strings for prediction table names
nm_method	string, prediction method used for IEDB prediction
nm_sht	string, short name of alleles
nm_fd	string, folder name which contains predict tables from IEDB
thold_score	list of vectors, binder thresholds by score
thold_rank	vector, binder thresholds by rank find_nonself_huII() find nonself binding peptides
dat_in	dataframe with pep_stim, core, pep_self selected from pull_ag_self

epitopR documentation built on Sept. 18, 2022, 1:07 a.m.