setData {Doscheda} | R Documentation

## Method for attaching and standardising data for objects of class 'ChemoProtSet'

### Description

This method will subset the orginal data set into the required columns, standardising column names in the process.

### Usage

    setData(x, dataFrame, dataChannels, accessionChannel, uniquePeps = NA,
      sequenceChannel = NA, qualityChannel = NA, pdofpdChannel = NA,
      incGeneID = FALSE, geneIDFile = NA)

    ## S4 method for signature 'ChemoProtSet'
    setData(x, dataFrame, dataChannels, accessionChannel,
      uniquePeps = NA, sequenceChannel = NA, qualityChannel = NA,
      pdofpdChannel = NA, incGeneID = FALSE, geneIDFile = NA)

### Arguments

`x` | object of class 'ChemoProtSet'
`dataFrame` | data.frame of the input data set
`dataChannels` | column names of dataFrame that correspond to data channels. These should be ordered in the format: rep1_concentration_0, ..., rep1_concentration_n, rep2_concentration_0, ...
`accessionChannel` | string that is the same as the column name for the protein accessions in dataFrame
`uniquePeps` | string that is the same as the column name for the number of unique peptides in dataFrame
`sequenceChannel` | string that is the same as the column name for the peptide sequences in dataFrame
`qualityChannel` | string that is the same as the column name for the peptide quality score in dataFrame
`pdofpdChannel` | string that is the same as the column name for the pull-down of pull-down data in dataFrame
`incGeneID` | boolean value indicating if a protein accession to gene ID file is supplied
`geneIDFile` | data.frame containing a protein accession to gene ID conversion file

### 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<- setData(x = ex, dataFrame = doschedaData, dataChannels = channelNames,
    accessionChannel = 'Master.Protein.Accessions',
    sequenceChannel = 'Sequence',qualityChannel = 'Qvality.PEP')

    ex

[Package Doscheda version 1.14.0 Index]