IPSSMprocess: Processing of user-defined clinical and molecular variables

In papaemmelab/ipssm: Molecular International Prognosis Scoring System For Myelodysplastic Syndromes

Processing of user-defined clinical and molecular variables

Description

Process clinical and molecular user-defined variables to model-based variables.

Usage

IPSSMprocess(
  patientInput,
  genesRes = c("BCOR", "BCORL1", "CEBPA", "ETNK1", "GATA2", "GNB1", "IDH1", "NF1",
    "PHF6", "PPM1D", "PRPF8", "PTPN11", "SETBP1", "STAG2", "WT1"),
  maxvafloh = 0.55,
  Nref = 0.388
)

Arguments

patientInput	a patient data.frame, one patient per row, and variables as columns.
genesRes	a vector containing the names of the residual genes.
maxvafloh	maximum variant allele frequency (vaf) threshold to determine theres Loss of Heterozigosity (LOH).
Nref	the average reference value for min(Nres,2) where Nres is the number of mutated residual genes.

Value

A processed patient data.frame, same number of rows/patients as in patientInput, and with the processed variables as additional columns.

Examples

dd <- read.csv(system.file("extdata", "IPSSMexample.csv", package = "ipssm"), header = TRUE)
dd.process <- IPSSMprocess(patientInput = dd)
print(dd.process)

papaemmelab/ipssm documentation built on Feb. 8, 2023, 3:09 p.m.