PTMestimate takes as input the summarized log2-intensities for each
PTM site, performs statistical modeling for the abundance of the site, and
returns the estimates of model parameters for all sites in all experimental
conditions. If protein log2-intensities are availble, the same estimation
procedure is applied to each protein as well.
A list of two data frames named
A logical defining the handling of batch effect for all data
or two logicals for the
A list of two lists named
PTM list has four elements:
protein (a string vector of
site (a string vector of PTM sites),
(a list of model parameter estimates for each site), and
numeric vector of degrees of freedom for each model). The
list includes all as in
1 2 3 4 5 6 7 8 9
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