"MasterPeptides"MasterPeptides-class.RdA class to store the results of makeMaster. This class
stored the 2 versions (orders) of the master final peptide data.
Objects can be created by calls of the form makeMaster.
masters:Object of class "list" storing the 2
master data.frame objects.
pepfiles:Object of class "character" with the
list of final peptide input files.
fdr:Object of class "numeric" with the
peptide false discovery applied when creating the filter.
method:Object of class "character" with the
peptide p-value adjustment method. One of BH (default),
qval or Bonferroni.
orders:Object of class "list" with the
numeric vectors specifying the order of pepfiles
used to generate the respective masters
data.frames.
fragmentfiles:Object of class "character" with the
list of final fragment input files.
fragments:Object of class data.frame storing the
combined final fragment data.
fragmentlibrary:Object of class "MSnExp" storing
the fragment library.
signature(object = "MasterPeptides"): to print a
textual representation of the instance.
Improving qualitative and quantitative performance for MSE-based label free proteomics, N.J. Bond, P.V. Shliaha, K.S. Lilley and L. Gatto, Journal of Proteome Research, 2013, in press.
The Effects of Travelling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies, P.V. Shliaha, N.J. Bond, L. Gatto and K.S. Lilley, Journal of Proteome Research, 2013, in press.