runDoscheda {Doscheda} | R Documentation |
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
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)