setParameters {Doscheda} | R Documentation

## Method to set parameters for a ChemoProtSet

### 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

[Package Doscheda version 1.10.4 Index]