Function reference • epitopefindr

Package Info epitopefindr package help file
`epitopefindr`	epitopefindr: a package for identifying minimal overlaps from BLAST alignments.
Main Function To execute a typical epitopefindr pipeline
`epfind()` `epFind2()`	All-in-one function to call the major steps of epitopefindr.
Sub Functions Execute smaller steps of epfind
`pbCycleBLAST()`	Initialize a txtProgressBar object with which to call cycleBLAST.
`cycleBLAST()`	Repeatedly call epitopeBLAST to iterate through all index peptides until all peptides are converted to trimmed epitopes.
`epitopeBLAST()`	Identifies next index peptide, calls indexEpitopes to parse alignments to that index peptide, and updates BLAST table accordingly.
`indexEpitopes()`	For a specified index peptide, identify the maximal intervals that represent the consensus overlap of reported BLAST alignments to that peptide. Update the BLAST table accordingly.
`trimEpitopes()`	Update BLAST table positions to reflect smaller intervals when a subinterval has been determined as the minimal overlap of alignments to a peptide.
`indexGroups()`	Group trimmed sequences into aligning groups
`groupMSA()`	Generate pdf multiple sequence alignment logos for identified aligning groups.
Helper Functions Smaller functions to perform simple operations
`addPepSeq()`	Add/update column in blast table listing peptide names.
`chooseIndex()`	Identifies which of a set of remaining peptides from a blast alignment table should serve as the next index peptide.
`decipherGaps()`	Split gapped BLAST alignments into smaller ungapped alignments.
`epitopefindrEnv`	.onload Set stringsAsFactors FALSE for epitopefindr
`epPB()`	Epitope progress bar, epPB calls utils::txtProgressBar with some standardized parameters to reduce redundancy.
`filterBLAST()`	Remove singletons, sequneces with no non-self alignments, from BLAST alignment table.
`isOverlapping()`	Checks whether the stard/end pos in pattern overlaps with the start/end pos of each row in table by at least almin and returns positions in table that overlap.
`makeIR()`	Converts a two-column data frame to an IRanges object for overlap calculations.
`mergeFastaDuplicates()`	If two fasta entries have the same sequence, keep only one copy of the sequence but concatenante the name to be Name1__Name2; __ can be replaced with delimiter of choice.
`numAlignments()`	Add/update column to blast table listing # of alignments per query sequence.
`organizeBLAST()`	Rename unwieldy columns from rBLAST output table.
`outputTable()`	Generates tables of reportable data on identified minimal alignments.
`prepareBLAST()`	Call series of functions to standardize BLAST table for computation.
`qsSwap()`	Swap query and subject data from a BLAST table.
`queryBLASTaa()`	BLAST query sequence against a database of sequences.
`removeSmallAln()`	Delete rows in blast table for which the alignment is fewer than 7aa or other custom threshold.
`renameBLAST()`	Revert qID and sID columns of blast table back to original names based on naming map.
`renameFasta()`	Revert peptide names of a fasta file back to original names based on naming map.
`selfBLASTaa()`	Run BLASTp on amino acid sequences against themselves.
`threshBLAST()`	Subset initial BLAST alignbment table to only include alignments below a specified e-value threshold.
`tidyBLAST()`	Call a series of functions to tidy raw BLAST alignment table for use.
`tidyFasta()`	Remove filler sequences after "." stop codon and cterminal "*"
`unmergeFastaDuplicates()`	If a fasta entry has a concatenated name, e.g. from a previous call to mergeFastaDuplicates, then separate the concatenanted name and make a separate entry for each.
`writeFastaAA()`	Takes data frame with $Seq and $ID or AAStringSet and writes fasta file
Data Example datasets
`pairwise_viral_hits`	Virscan hits from AVARDA patient 1

Reference

Package Info

Main Function

Sub Functions

Helper Functions

Data