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

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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## 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.