groupMSA.Rd
Generate pdf multiple sequence alignment logos for identified aligning groups.
groupMSA(
groups,
mpath = "intermediate_files/msa/",
min.groupsize = 2,
min.consensus.pos = 1,
consensus.type = "Biostrings",
consensus.thresh = c(100, 49),
peptide.nchar = 50,
msa.width = "dynamic",
pdflatex = TRUE,
pdftk = TRUE,
pdfuniter = FALSE,
make.png = FALSE
)
Table of final peptides and pre-calculated groupings.
Directory to write sequence alignment files.
Minimum number of peptides per group to require in order to print a group.
Minimum number of amino acid consensus positions required in order to print a group.
"upperlower" or "Biostrings" type of msa consensus sequence to output
Two decreasing numeric values of upper and lower thresholds for sequence consensus. ONly valid for consensus.type == "upperlower".
Maximum of character from peptide name to use in msa output. Default 50. Starts from left.
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.
Logical whether or not to produce PDF LaTeX figures using pdflatex
Logical whether or not to use staplr and pdftk to merge individual msa pdfs.
Logical whether or not to merge msa pdfs using staplr and pdfuniter
Locial whether or not to convert PDF output to PNG.