epfind: All-in-one function to call the major steps of epitopefindr.

In brandonsie/epitopefindr: Minimal Overlaps from BLAST Alignments

All-in-one function to call the major steps of epitopefindr.

Description

All-in-one function to call the major steps of epitopefindr.

Usage

epfind(
  data = NULL,
  output.dir = NULL,
  e.thresh = 0.01,
  g.method = "any",
  aln.size = 7,
  min.groupsize = 2,
  min.consensus.pos = 1,
  consensus.type = "Biostrings",
  consensus.thresh = c(100, 49),
  peptide.nchar = 50,
  msa.width = "dynamic",
  verbose = TRUE,
  pdflatex = TRUE,
  pdftk = FALSE,
  pdfuniter = TRUE,
  make.png = FALSE,
  name.msa = "msa.pdf",
  name.alignments = "finalAlignments.csv",
  name.epitopekey = "epitopeKey.csv",
  name.epitopesum = "epitopeSummary.csv",
  use.doParallel = FALSE,
  delete.intermediates = FALSE
)

epFind2(
  data = NULL,
  output.dir = NULL,
  e.thresh = 0.01,
  g.method = "any",
  aln.size = 7,
  min.groupsize = 2,
  min.consensus.pos = 1,
  consensus.type = "Biostrings",
  consensus.thresh = c(100, 49),
  peptide.nchar = 50,
  msa.width = "dynamic",
  verbose = TRUE,
  pdflatex = TRUE,
  pdftk = FALSE,
  pdfuniter = TRUE,
  make.png = FALSE,
  name.msa = "msa.pdf",
  name.alignments = "finalAlignments.csv",
  name.epitopekey = "epitopeKey.csv",
  name.epitopesum = "epitopeSummary.csv",
  use.doParallel = FALSE,
  delete.intermediates = FALSE
)

Arguments

data	Biostrings::AAStringset input sequences to search for epitopes, or path to corresponding .fasta file.
output.dir	Directory to which output files should be written.
e.thresh	Maximum e-value to consider from BLASTp alignments of 'data'.
g.method	Grouping method of alignments. Either 'any' or 'all'. See ?indexGroups
aln.size	Minimum length of alignment to consider from BLASTp alignments of 'data'.
min.groupsize	Minimum number of peptides per group to require in order to print a group.
min.consensus.pos	Minimum number of amino acid consensus positions required in order to print a group.
consensus.type	"upperlower" or "Biostrings" type of msa consensus sequence to output
consensus.thresh	Two decreasing numeric values of upper and lower thresholds for sequence consensus.
peptide.nchar	Maximum of character from peptide name to use in msa output. Default 50. Starts from left.
msa.width	Controls whether or not MSA images have fixed or dynamic width. By default, msa.width is set to "dynamic", which causes the document dimentions of the resultant image to be calculated based on the lentht of the peptide name and the number of amino acids in the sequence alignment. If msa.width is instead set to a numeric, then an MSA will be printed with a fixed with that number of inches. With 50-character peptide.nchar and a maximum expected sequence alignment of 45 positions, an msa.width of 12 is more than sufficient.
verbose	Logical to print progress updates.
pdflatex	Logical whether or not to produce PDF LaTeX figures using pdflatex
pdftk	Logical whether or not to merge msa pdfs using staplr and pdftk
pdfuniter	Logical whether or not to merge msa pdfs using staplr and pdfuniter
make.png	Locial whether or not to convert PDF output to PNG.
name.msa	Filename for output merged pdf of msa logos.
name.alignments	Filename for output spreadsheet of peptide alignments.
name.epitopekey	Filename for output spreadhseet of epitopes per peptide.
name.epitopesum	Filename for output summary sheet of epitopes.
use.doParallel	Logical whether or not to use doParallel parallelization.
delete.intermediates	Logical whether or not to delete the intermediate_files folder at the end

brandonsie/epitopefindr documentation built on May 4, 2024, 10:27 a.m.