GMMres-class: Processed MS data

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Processed MS data

Description

This class contains the MS data to be used, after pre-processing and Gaussian Mixture Modelling

Objects from the Class

Objects of class GMMres can be created from new("GMMres", res=GMM.res, IDmap=GMM.res.ID)

Slots

res:

result of the Gaussian mixture modelling process, i.e. a list with an element for each peptide, each element containing a matrix with: the P/C cluster assignment ("clus"), log likelihood of P/C ("Indiv"), adjusted p value of FC drug vs ctrl ("FCvCaPval") and OK/FP/FN/I status ("status")

IDmap:

a data frame that maps the data identifiers (column "dataID", names of the elements in the res list) to the network identifiers (column "S.cc", UPID.res.pos)

resFC:

same as res but with an extra column in each matrix, containing the value of the fold changes

Methods

An overview of methods with class-specific functionality: More detailed introduction can be found in help for each specific function.

dataBycond

reorganise the data to have a matrix for each drug treatment, as elements of a list with an entry for each condition (set of drug targets that are shared between different treatments)

Author(s)

C. Terfve [e-mail]

See Also

dataBycond

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.