removePeptides {Doscheda} | R Documentation |
Method to remove peptides from input data of an object of class 'ChemoProtSet'
removePeptides(x, changePearson = NA, removePeps = TRUE) ## S4 method for signature 'ChemoProtSet' removePeptides(x, changePearson = NA, removePeps = TRUE)
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 |
object of class ChemoProtSet
## 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)