Usage
PharmacoSet(name, molecularProfiles = list(), cell = data.frame(), drug = data.frame(), sensitivityInfo = data.frame(), sensitivityRaw = array(dim = c(0, 0, 0)), sensitivityProfiles = matrix(), sensitivityN = matrix(nrow = 0, ncol = 0), perturbationN = array(NA, dim = c(0, 0, 0)), curationDrug = data.frame(), curationCell = data.frame(), curationTissue = data.frame(), datasetType = c("sensitivity", "perturbation", "both"), verify = TRUE)
Arguments
name
A character string detailing the name of the dataset
molecularProfiles
A list of ExpressionSet objects containing
molecular profiles
cell
A data.frame containg the annotations for all the cell
lines profiled in the data set, across all data types
drug
A data.frame containg the annotations for all the drugs
profiled in the data set, across all data types
sensitivityInfo
A data.frame containing the information for the
sensitivity experiments
sensitivityRaw
A 3 Dimensional array contaning the raw drug
dose response data for the sensitivity experiments
sensitivityProfiles
data.frame containing drug sensitivity profile
statistics such as IC50 and AUC
sensitivityN, perturbationN
A data.frame summarizing the
available sensitivity/perturbation data
curationDrug, curationCell, curationTissue
A data.frame mapping
the names for drugs, cells and tissues used in the data set to universal
identifiers used between different PharmacoSet objects
datasetType
A character string of 'sensitivity',
'preturbation', or both detailing what type of data can be found in the
PharmacoSet, for proper processing of the data
verify
boolean Should the function verify the PharmacoSet and
print out any errors it finds after construction?