removePeptides-methods: Method to remove peptides from input data of an object of...

In brunocontrino/DOSCHEDA: A DownStream Chemo-Proteomics Analysis Pipeline

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)

brunocontrino/DOSCHEDA documentation built on Sept. 15, 2020, 12:12 a.m.