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