VolcanoPam: Visualize Output Object from AutoPamGeneMix

In pamgene/PamGeneMixed: Preprocessing and Modeling Kinase Activity Profiles in PamChip Data

Description

This function visualizes Volcano plots of p-values returns from the AutoPamGeneMix. It also returns Top K Peptides according to the test at t=0, t=end, t=any time point, and t=entire profile. Corresponding p-values are also returned.

Usage

VolcanoPam(ObjectAutoPam,Topp=5,plotting=TRUE)

Arguments

ObjectAutoPam	Object out from the AutoPamGeneMix.
Topp	Number of top K peptides to be considered. Default is five.
plotting	A boolean parameter indicating whether the plots to be shown.

Value

PP	A data frame with p-values.
TopList	Top K peptides at time points where the tests are performed.

Author(s)

Pushpike Thilakarathne, Ziv Shkedy and Dan Lin

See Also

AutoPamGeneMix

Examples

#--------


    data(PamChipData)
    
    PeptidesNames<-setdiff(colnames(PamChipData),
        c("ID", "ResState", "ArrayNum", "CellName", "TreatName","Time"))


 #------- Four groups in the data ---
    # Apply preprocessing steps for each peptide
    temp2<-PreProcessAllPeptides(pep.names=PeptidesNames,PamSig=PamChipData,PathOutPut="C:/Temp")
    
    #-----------------------------------
    #  Fit the model for each peptide : This will take a while !!
    ResultsAll<-AutoPamGeneMix(formula=y~-1+ResTrt+s(time,by=ResTrt,bs="tp",m=3),
    Weights=varIdent(form=~1|ResTrt),
    Random.structure=list(ArrayNum=~1,CellLineResTrt=~1+time+time2,ID=~1+time+time2),
    temp2,TestAt=30,PathOutPut="C:/FittedGamm")
    
    show(ResultsAll)
    
    
    #---------------------------------
    VolcanoPam(ResultsAll,Topp=10,plotting=FALSE)
    
    #---------------------------------
    VolcanoPam(ResultsAll,Topp=5,plotting=TRUE)
 

pamgene/PamGeneMixed documentation built on Dec. 31, 2020, 1:13 a.m.