setData-methods: Method for attaching and standardising data for objects of...

In brunocontrino/Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

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

brunocontrino/Doscheda documentation built on Sept. 14, 2020, 4:45 p.m.