## ----setParametersEx, eval = TRUE--------------------------------------------- library(Doscheda) channelNames <- c("Abundance..F1..126..Control..REP_1", "Abundance..F1..127..Sample..REP_1", "Abundance..F1..128..Sample..REP_1", "Abundance..F1..129..Sample..REP_1", "Abundance..F1..130..Sample..REP_1", "Abundance..F1..131..Sample..REP_1", "Abundance..F2..126..Control..REP_2", "Abundance..F2..127..Sample..REP_2", "Abundance..F2..128..Sample..REP_2", "Abundance..F2..129..Sample..REP_2", "Abundance..F2..130..Sample..REP_2", "Abundance..F2..131..Sample..REP_2") ex <- new('ChemoProtSet') ex<- setParameters(x = ex,chansVal = 6, repsVal = 2, dataTypeStr = 'intensity', modelTypeStr = 'linear', PDBool = FALSE,removePepsBool = FALSE,incPDofPDBool = FALSE, incGeneFileBool = FALSE,organismStr = 'H.sapiens', pearsonThrshVal = 0.4) ## ----setDataEx, eval = TRUE--------------------------------------------------- ex<- setData(x = ex, dataFrame = Doscheda::doschedaData, dataChannels = channelNames, accessionChannel = "Master.Protein.Accessions", sequenceChannel = 'Sequence', qualityChannel = "Qvality.PEP" ) ## ----peptideRemovalExample, eval = TRUE--------------------------------------- ex <- removePeptides(ex,removePeps = FALSE) ## ----fitModelEx, eval = TRUE, include=FALSE----------------------------------- ex<- runNormalisation(ex) ex <- fitModel(ex) ## ----runDosEx, eval = FALSE--------------------------------------------------- # # channelNames <- c("Abundance..F1..126..Control..REP_1", # "Abundance..F1..127..Sample..REP_1", "Abundance..F1..128..Sample..REP_1", # "Abundance..F1..129..Sample..REP_1", "Abundance..F1..130..Sample..REP_1", # "Abundance..F1..131..Sample..REP_1", "Abundance..F2..126..Control..REP_2", # "Abundance..F2..127..Sample..REP_2", "Abundance..F2..128..Sample..REP_2", # "Abundance..F2..129..Sample..REP_2", "Abundance..F2..130..Sample..REP_2", # "Abundance..F2..131..Sample..REP_2") # # ex <- runDoscheda(dataFrame = doschedaData, dataChannels = channelNames, # chansVal = 6, repsVal = 2,dataTypeStr = 'intensity', # modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE, # accessionChannel = "Master.Protein.Accessions", # sequenceChannel = 'Sequence',qualityChannel = "Qvality.PEP", # incPDofPDBool = FALSE, incGeneFileBool = FALSE, # organismStr = 'H.sapiens', pearsonThrshVal = 0.4) # # runDoscheda() # ## ----plot1-------------------------------------------------------------------- plot(ex) ## ----boxPlot------------------------------------------------------------------ boxplot(ex) ## ----corrplot----------------------------------------------------------------- corrPlot(ex) ## ----pcaplot------------------------------------------------------------------ pcaPlot(ex) ## ----repplot------------------------------------------------------------------ replicatePlot(ex,conc = 0, repIndex1 = 1, repIndex2 = 2) ## ----colcanolot--------------------------------------------------------------- volcanoPlot(ex) ## ----meanolcanolot------------------------------------------------------------ meanSdPlot(ex) ## ----exampleR, eval = FALSE--------------------------------------------------- # channelNames <- c("Abundance..F1..126..Control..REP_1", # "Abundance..F1..127..Sample..REP_1", "Abundance..F1..128..Sample..REP_1", # "Abundance..F1..129..Sample..REP_1", "Abundance..F1..130..Sample..REP_1", # "Abundance..F1..131..Sample..REP_1", "Abundance..F2..126..Control..REP_2", # "Abundance..F2..127..Sample..REP_2", "Abundance..F2..128..Sample..REP_2", # "Abundance..F2..129..Sample..REP_2", "Abundance..F2..130..Sample..REP_2", # "Abundance..F2..131..Sample..REP_2") # ex <- new('ChemoProtSet') # ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,dataTypeStr = 'intensity', # modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE, # incPDofPDBool = FALSE,incGeneFileBool = FALSE,organismStr = 'H.sapiens', pearsonThrshVal = 0.4) # ex<- setData(x = ex, dataFrame = doschedaData, dataChannels = channelNames, # accessionChannel = "Master.Protein.Accessions", # sequenceChannel = 'Sequence', qualityChannel = "Qvality.PEP" ) # ex <- removePeptides(ex,removePeps = FALSE) # ex <- runNormalisation(ex) # ex <- fitModel(ex) # ex