R: Computes FDR for all possible final peptide combinations
estimateMasterFdr
R Documentation
Computes FDR for all possible final peptide combinations
Description
This function takes all possible combination of 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.
A numeric indicating the maximum merged
false discovery to be allowed.
fdr
Peptide FDR level for individual peptide files filtering.
proteotypic
Logical. Should number proteotypic peptides be
used to choose best combination and plot results or total number
of unique peptides.
missedCleavages
Number of missed cleavage sites. Default is 0.
verbose
Should progress messages be printed?
Details
The false discovery rate for the master (merged) file is calcualted
by summing the number of estimated false discoveries for each
individual final peptide file (number of unique peptides in that file
multiplied by fdr) divided by the total number of unique
peptides for that specific combination.
The function returns an instance of the class
"MasterFdrResults".
Value
An instance of class "MasterFdrResults".
See details above.
Author(s)
Laurent Gatto
References
Bond N. J., Shliaha P.V., Lilley K.S. and Gatto L.,
(2013) J. Prot. Research.
See Also
The 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.