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

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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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.