makeMaster(pepfiles, fdr = 0.01, method = c("BH", "Bonferroni", "qval"),
span = 0.05, verbose = TRUE)
list
of peptide final peptide file names
to be merged.numeric
indicating the preptide false
discovery rate limit.character
indicating the p-value adjustment to
be used. One of BH
(default), Bonferroni
or qval
.numeric
with the loess span parameter value
to be used for retention time modelling.logical
indicating information should be
printed out."MasterPeptides "
.fdrand (iii) proteins with a false
positive rate <=fpr.==
MasterPeptides
instance.The resulting MasterPeptides
instance can be further used
for a complete master vs. peptides/Pep3D analysis, as described in
Synapter
, synergise
or using the GUI
(synapterGUI
). To do so, it must be serialised (using the
saveRDS
function) with a .rds
file
extension, to be recognised (and loded) as a R
object.
When several quantitation (or identification) files are combined as a master set to be mapped back against the inidividual final peptide files, the second master [P2, P3, P1] is used when analysing the peptide data that was first selected in the master generation (P1 above). This is to avoid aligning two identical sets of peptides (those of P1) and thus not being able to generate a valid retention time model. This is detected automatically for the user.
The two master peptides dataframes can be exported to disk as
two csv
files with writeMasterPeptides
. The
MasterPeptides
object returned by makeMaster
can be
saved to disk (with save
or saveRDS
) and later reloaded
(with load
or readRDS
) for further analysis.
Synapter
class manual page for
detailed information on filtering and modelling and the general
algorithm implemented in the synapter
package.The estimateMasterFdr
function allows to control
false dicovery rate when combining several peptide files while
maximising the number of identifications and suggest which
combination of peptide files to use.
The vignette, accessible with synapterGuide()
illustrates a complete pipeline using estimateMasterFdr
and
makeMaster
.