Import clinical information for a patient

Import clinical information for a patient

import_clinical(clinicalData = NA, patientID = NA, extract_column)

Arguments

clinicalData	data frame containing the clinical information for a patient. This needs to include a column `SampleName` containing unique names for all the RNA-Seq samples available in the cohort; a `PID` column for patient ID and a `Time` column that should reflect the time of sample collection.
patientID	a character vector specifying the patient id for which clinical data should be imported.
extract_column	vector specifying the column to be extracted. Currently only numeric variables with values between 0 and 1 are allowed to be consistent with plotting together with clonality and VAF estimates.

Value

The function returns a data fram where only `SampleName`, `PID`, `Time` and the variable of interest `extract_column` are kept as well as new variables `VAF`, `mutation_key` and `mutation_det` are added. In this way, clinical information, like tumour purity, is stored in the same way as the variants created with `import_any()` and can be easily combined and plotted together. At the moment, the structure expects `extract_column` to be in the 0-1 range to be consistent with te fact that usually the Variant Allele Frequency (VAF) for a variant is plotted over time.

Examples

clinicalData <- data.frame(SampleName = c("D1.Screen.Rel","D1.Cyc1.Rel",
                                          "D1.Cyc2.Rel","D1.Cyc3.Rel"),
                           PID = "D1",
                           Time = c("Screen", "Cyc1","Cyc2","Cyc3"),
                           Outcome = "Rel",
                           AgeDiagnosis = 65,
                           Sex = "F",
                           Blast = c(80,5,7,40)/100)

import_blast <- import_clinical(clinicalData = clinicalData,
extract_column = "Blast",
patientID = "D1")