# #——setParametersEx, eval = TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(Doscheda) channelNames < - c(126年“F1丰富. . . . . .控制. .REP_1”、“丰富. . F1 . . 127 . .样品. .REP_1”、“丰富. . F1 . . 128 . .样品. .REP_1”、“丰富. . F1 . . 129 . .样品. .REP_1”、“丰富. . F1 . . 130 . .样品. .REP_1”、“丰富. . F1 . . 131 . .样品. .REP_1”、“丰富. . F2…126…控制. .REP_2”、“丰富…F2样本…127……REP_2”、“丰富…F2样本…128……REP_2”、“丰富…F2样本…129……REP_2”、“丰富…F2样本…130……REP_2”、“丰富…F2…131…样本…REP_2”) < -新交货(ChemoProtSet) < -交货setParameters (x =前,chansVal = 6, repsVal = 2, dataTypeStr =“强度”,modelTypeStr =“线性”,PDBool = FALSE, removePepsBool = FALSE, incPDofPDBool = FALSE, incGeneFileBool = FALSE, organismStr = ' H。智人,pearsonThrshVal = 0.4) # #——setDataEx, eval = TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - < -交货setData (x =前,dataFrame = Doscheda: doschedaData, dataChannels = channelNames accessionChannel = " Master.Protein。登记入册”,sequenceChannel =‘序列’,qualityChannel = " Qvality。PEP) # #——peptideRemovalExample, eval = TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <交货- removePeptides (ex removePeps = FALSE) # #——fitModelEx, eval = TRUE,包括= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - < - runNormalisation交货(交货)例<——fitModel(特异)# #——runDosEx, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # channelNames < - c(126年“F1丰富. . . . . .控制. .REP_1”#“丰富. . F1 . . 127 . .样品. .REP_1”、“丰富. . F1 . . 128 . .样品. .REP_1”#“丰富. . F1 . . 129 . .样品. .REP_1”、“丰富. . F1 . . 130 . .样品. .REP_1”#“丰富. . F1 . . 131 . .样品. .REP_1”、“丰富. . F2…126…控制. .REP_2”#“富足…F2样本…127……REP_2”、“丰富…F2样本…128……REP_2”#“富足…F2样本…129……REP_2”、“丰富…F2样本…130……REP_2”#“富足…F2…131…样本…REP_2”) # # < - runDoscheda交货(dataFrame = doschedaData dataChannels = channelNames # chansVal = 6, repsVal = 2, dataTypeStr =“强度”,# modelTypeStr =“线性”,PDBool = FALSE, removePepsBool = FALSE, # accessionChannel = " Master.Protein。登记入册”,# sequenceChannel =‘序列’,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