fitModel {Doscheda} | R Documentation

## Method to fit a model to an object of class 'ChemoProtSet'

### Description

Method to fit a model to an object of class 'ChemoProtSet'

### Usage

    fitModel(x)

    ## S4 method for signature 'ChemoProtSet'
    fitModel(x)

### Arguments

`x` | object of class 'ChemoProtSet'

### Value

object of class ChemoProtSet

### See Also

`DoschedaSet`

### Examples

    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

    ex <- processedExample
    ex <- runNormalisation(ex)
    ex <- fitModel(ex)

    ex

[Package Doscheda version 1.9.2 Index]