setParameters-methods: Method to set parameters for a ChemoProtSet

In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

Description

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

Usage

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

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

Doscheda documentation built on Nov. 8, 2020, 5:37 p.m.