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 |