Minimal Protein Set Explaining Peptide Spectrum Matches
Readjust windows so that boundaries in regions of few peaks.
wrapper setting the correct parameters seqinr::read.fasta for reading ...
remove signal peptides from main chain
create rev sequences to fasta list
write fasta lists into file
annotate peptides using AhoCorasickTrie
Annotate peptides with protein ids
Compute dynamic swath windows
Compute FDR given a score
Compute FDR given a score
create fasta db from one or more fasta files
Create db with decoys and contaminants
given matrix (columns protein rows peptides), compute minimal protein ...
converts result of greedy function to a matrix with 3 columns - peptid...
tests hard constraints
load list of contaminant sequences FGCZ 2019
load list of contaminant sequences FGCZ 2021
make id for chain in format sp|P30443|1A01_HUMANs25
make id for chain compatible with uniprot
compute the deviation from optimum: equal number of MS1 per bin
plot FDR
Predict score given FDR
given table of peptide protein assigments generate matrix
Small version of pepprot dataset to speed up computation
Minimal Protein Set Explaining Peptides
Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants. Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.