|
annotateAHO()
|
annotate peptides using AhoCorasickTrie |
|
annotatePeptides()
|
Annotate peptides with protein ids |
|
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 |