setParameters-methods: Method to set parameters for a ChemoProtSet

Description Usage Arguments Value See Also Examples

Description

Give the ChemoProtSet object the correct parameters for a given experiment in order to successfully run the pipelin

Usage

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setParameters(x, chansVal, repsVal, dataTypeStr, modelTypeStr, PDBool = TRUE,
  removePepsBool = NA, incPDofPDBool = FALSE, PDofPDname = NA,
  incGeneFileBool = FALSE, organismStr = "h.sapiens", sigmoidConc = NA,
  pearsonThrshVal = 0.4)

## S4 method for signature 'ChemoProtSet'
setParameters(x, chansVal, repsVal, dataTypeStr,
  modelTypeStr, PDBool = TRUE, removePepsBool = NA, incPDofPDBool = FALSE,
  PDofPDname = NA, incGeneFileBool = FALSE, organismStr = "h.sapiens",
  sigmoidConc = NA, pearsonThrshVal = 0.4)

Arguments

x

object of class 'ChemoProtSet'

chansVal

number of channels / concentrations in experiment

repsVal

number of replicates in experiment

dataTypeStr

string describing the data type of input data set. This can be 'LFC' for log fold-changes, 'FC' for fold-changes and 'intensity' for peptide intensities

modelTypeStr

string describing the type of model applied. This can be 'linear' for a linear model or 'sigmoid' for a sigmoidal model

PDBool

boolean value indicating if the input data is from Proteome Discoverer 2.1 or not

removePepsBool

boolean value indicating if peptide removal will take place. Only valid if input data is peptide intensities

incPDofPDBool

boolean value indicating if the input data contais a pull-down of pull-down colum

PDofPDname

string with the same name as colulmn containing pull-down of pull-down data. NA if this is not applicable

incGeneFileBool

boolean value indicating if the data requires a protein accession to gene ID conversion file

organismStr

string giving the name of organism. the options are: 'H.sapiens', 'D. melanogaster', 'C. elegans', 'R. norvegicus', 'M. musculus'. This is only needed if PDbool is FALSE

sigmoidConc

vector of numerical values for concentrations of channels in the case of a sigmoidal fit

pearsonThrshVal

numerial value between -1 and 1 which determines the cut-off used to discard peptides during peptide removal

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

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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

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