runDoscheda {Doscheda} | R Documentation

## Wrapper Function to run the entire Doscheda pipeline

### Description

A wrapper for the whole Doscheda pipeline, if users want to avoid using the separate steps.

### Usage

    runDoscheda(dataFrame, dataChannels, accessionChannel, chansVal, repsVal,
      dataTypeStr, modelTypeStr, PDBool = TRUE, removePepsBool = NA,
      incPDofPDBool = FALSE, PDofPDname = NA, incGeneFileBool = FALSE,
      organismStr = "h.sapiens", sigmoidConc = NA, pearsonThrshVal = 0.4,
      uniquePeps = NA, sequenceChannel = NA, qualityChannel = NA,
      pdofpdChannel = NA, incGeneID = FALSE, geneIDFile = NA,
      normType = "loess")

### Arguments

`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
`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
`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
`normType` | string indicating the type of normalisation that should take place ('loess', 'median', 'none')

### 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 <- runDoscheda(dataFrame = doschedaData, dataChannels = channelNames,
    chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
    modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
    accessionChannel = 'Master.Protein.Accessions',
    sequenceChannel = 'Sequence',qualityChannel = 'Qvality.PEP',
    incPDofPDBool = FALSE, incGeneFileBool = FALSE,
     organismStr = 'H.sapiens', pearsonThrshVal = 0.4)

[Package Doscheda version 1.12.0 Index]