utils: Basic functions of the package
In epitopeR: Predict Peptide-MHC Binding

utils

R Documentation

Basic functions of the package

Description

val_ag_name() validation of name of binding locus

Usage

val_ag_name(ag_present)

preproc(allele_in, link)

pull_seq(alleles_in, tbl_ref_in)

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

comb_pred_tbl_mhcI(nm_method, nm_fd, thold_score, thold_rank)

find_nonself(dat_in)

pull_ag_self(vec_in)

find_core_mut(dat_in)

align_seq(seq1, seq2, gapopening = 0, gapextension = 8)

pull_obj_name(x)

Arguments

`ag_present`	a vector of locus name(s) to make binding predictions for preproc() format and validate allele names
`allele_in`	a vector contains allele name(s)
`link`	a string of url of MHC I or II api pull_seq() pull out sequence of each allele based on ref table
`alleles_in`	vector, allele names
`tbl_ref_in`	dataframe, reference table, default is human_all.csv from github comb_pred_tbl() combine individual prediction tables by method, exclude none-binders and keep strong and weak binders only
`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 ic50 score
`thold_rank`	vector, binder thresholds by percentile rank find_nonself() find nonself binding peptides
`dat_in`	dataframe with pep_stim, core, pep_self selected from pull_ag_self align_seq() align protein sequences
`vec_in`	dataframe with pep_stim, core, aligned ag_stim and ag_self columns find_core_mut() find mutation position to core
`seq1`	string, unaligned sequence of ag_stim
`seq2`	string, unaligned sequence of ag_self
`gapopening`	numeric, the cost for opening a gap in the alignment.
`gapextension`	numeric, the incremental cost incurred along the length of the gap in the alignment pull_obj_name()
`x,`	name of an object