setData {Doscheda} | R Documentation |
This method will subset the orginal data set into the required columns, standardising column names in the process.
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)
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 |
object of class ChemoProtSet
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