Minimal Protein Set Explaining Peptide Spectrum Matches

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Documentation for package ‘prozor’ version 0.3.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotateAHO	annotate peptides using AhoCorasickTrie
annotatePeptides	Annotate peptides with protein ids
Cdsw	Compute dynamic swath windows
Cdsw-class	Compute dynamic swath windows
computeFDR	Compute FDR given a score
computeFDRwithID	Compute FDR given a score
createDecoyDB	Create db with decoys and contaminants
create_fgcz_fasta_db	create fasta db from one or more fasta files
fdrSample	Data frame score and proteinID
greedy	given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithm
greedyRes2Matrix	converts result of greedy function to a matrix with 3 columns - peptide - charge and protein
loadContaminantsFasta2019	load list of contaminant sequences FGCZ 2019
loadContaminantsFasta2021	load list of contaminant sequences FGCZ 2021
makeID	make id for chain in format sp|P30443|1A01_HUMANs25
makeIDUnip	make id for chain compatible with uniprot
masses	MS masses A dataset containing approx 150000 MS1 precursor masses
objectiveMS1Function	compute the deviation from optimum: equal number of MS1 per bin
pepprot	Table containing peptide information
plotFDR	plot FDR
predictScoreFDR	Predict score given FDR
prepareMatrix	given table of peptide protein assigments generate matrix
protpepmetashort	Small version of pepprot dataset to speed up computation
prozor	Minimal Protein Set Explaining Peptides
readjustWindows	Readjust windows so that boundaries in regions of few peaks.
readPeptideFasta	wrapper setting the correct parameters seqinr::read.fasta for reading peptide sequences
removeSignalPeptide	remove signal peptides from main chain
reverseSeq	create rev sequences to fasta list
writeFasta	write fasta lists into file