removePeptides {Doscheda} | R Documentation

## Method to remove peptides from input data of an object of class 'ChemoProtSet'

### Description

Method to remove peptides from input data of an object of class 'ChemoProtSet'

### Usage

    removePeptides(x, changePearson = NA, removePeps = TRUE)

    ## S4 method for signature 'ChemoProtSet'
    removePeptides(x, changePearson = NA,
      removePeps = TRUE)

### Arguments

`x` | object of class 'ChemoProtSet'
`changePearson` | option to change the peasrson threshold cut-off parameter
`removePeps` | boolean value indicating whether peptide removal should take place

### Value

object of class ChemoProtSet

### See Also

`DoschedaSet`

### Examples

    ## Not run:
    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

    ## End(Not run)

[Package Doscheda version 1.12.0 Index]