pepfiles
of length greater or equal than 2 and computes the number of
estimated incorrect petides, the number of unique peptides,
the number of unique protetypic peptides and the
false discovery rate after merging for each combination.
The best combination has an fdr lower than masterFdr
and the highest number of unique (proteotypic) peptides.estimateMasterFdr(pepfiles, fastafile, masterFdr = 0.025, fdr = 0.01,
proteotypic = TRUE, missedCleavages = 0, verbose = TRUE)
list
of vector
of final peptide
filenames.character
with the fasta filename.numeric
indicating the maximum merged
false discovery to be allowed."MasterFdrResults "
.
See details above.fdr
) divided by the total number of unique
peptides for that specific combination.The function returns an instance of the class
"
.
makeMaster
function to combine
the peptide data as suggested by estimateMasterFdr
into
one single master peptide file.The vignette, accessible with synapterGuide()
illustrates a
complete pipeline using estimateMasterFdr
and
makeMaster
.