Package Infoepitopefindr package help file |
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epitopefindr: a package for identifying minimal overlaps from BLAST alignments. |
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Main FunctionTo execute a typical epitopefindr pipeline |
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All-in-one function to call the major steps of epitopefindr. |
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Sub FunctionsExecute smaller steps of epfind |
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Initialize a txtProgressBar object with which to call cycleBLAST. |
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Repeatedly call epitopeBLAST to iterate through all index peptides until all peptides are converted to trimmed epitopes. |
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Identifies next index peptide, calls indexEpitopes to parse alignments to that index peptide, and updates BLAST table accordingly. |
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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. |
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Update BLAST table positions to reflect smaller intervals when a subinterval has been determined as the minimal overlap of alignments to a peptide. |
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Group trimmed sequences into aligning groups |
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Generate pdf multiple sequence alignment logos for identified aligning groups. |
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Helper FunctionsSmaller functions to perform simple operations |
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Add/update column in blast table listing peptide names. |
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Identifies which of a set of remaining peptides from a blast alignment table should serve as the next index peptide. |
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Split gapped BLAST alignments into smaller ungapped alignments. |
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.onload Set stringsAsFactors FALSE for epitopefindr |
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Epitope progress bar, epPB calls utils::txtProgressBar with some standardized parameters to reduce redundancy. |
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Remove singletons, sequneces with no non-self alignments, from BLAST alignment table. |
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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. |
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Converts a two-column data frame to an IRanges object for overlap calculations. |
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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. |
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Add/update column to blast table listing # of alignments per query sequence. |
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Rename unwieldy columns from rBLAST output table. |
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Generates tables of reportable data on identified minimal alignments. |
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Call series of functions to standardize BLAST table for computation. |
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Swap query and subject data from a BLAST table. |
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BLAST query sequence against a database of sequences. |
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Delete rows in blast table for which the alignment is fewer than 7aa or other custom threshold. |
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Revert qID and sID columns of blast table back to original names based on naming map. |
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Revert peptide names of a fasta file back to original names based on naming map. |
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Run BLASTp on amino acid sequences against themselves. |
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Subset initial BLAST alignbment table to only include alignments below a specified e-value threshold. |
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Call a series of functions to tidy raw BLAST alignment table for use. |
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Remove filler sequences after "." stop codon and cterminal "*" |
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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. |
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Takes data frame with $Seq and $ID or AAStringSet and writes fasta file |
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DataExample datasets |
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Virscan hits from AVARDA patient 1 |