runDoscheda: Wrapper Function to run the entire Doscheda pipeline
In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

Description Usage Arguments Value See Also Examples

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

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")

`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')

object of class ChemoProtSet

DoschedaSet

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)