IPSSMwrapper: IPSS-M Wrapper

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

IPSS-M Wrapper

Description

Function that reads, processes, calculates and annotates to output IPSS-M results

Usage

IPSSMwrapper(
  path.file,
  sheet = 1,
  genesRes = c("BCOR", "BCORL1", "CEBPA", "ETNK1", "GATA2", "GNB1", "IDH1", "NF1",
    "PHF6", "PPM1D", "PRPF8", "PTPN11", "SETBP1", "STAG2", "WT1"),
  Nref = 0.388,
  betaValues = c(HB1 = -0.171, TRANSF_PLT100 = -0.222, BLAST5 = 0.352, CYTOVEC = 0.287,
    TP53multi = 1.18, FLT3 = 0.798, MLL_PTD = 0.798, SF3B1_5q = 0.504, NPM1 = 0.43, RUNX1
    = 0.423, NRAS = 0.417, ETV6 = 0.391, IDH2 = 0.379, CBL = 0.295, EZH2 = 0.27, U2AF1 =
    0.247, SRSF2 = 0.239, DNMT3A = 0.221, ASXL1 = 0.213, KRAS = 0.202, SF3B1_alpha =
    -0.0794, nRes2 = 0.231),
  meanValues = c(HB1 = 9.87, TRANSF_PLT100 = 1.41, BLAST5 = 0.922, CYTOVEC = 1.39,
    TP53multi = 0.071, FLT3 = 0.0108, MLL_PTD = 0.0247, SF3B1_5q = 0.0166, NPM1 = 0.0112,
    RUNX1 = 0.126, NRAS = 0.0362, ETV6 = 0.0216, IDH2 = 0.0429, CBL = 0.0473, EZH2 =
    0.0588, U2AF1 = 0.0866, SRSF2 = 0.158, DNMT3A = 0.161, ASXL1 = 0.252, KRAS = 0.0271,
    SF3B1_alpha = 0.186, nRes2 = 0.388),
  bestValues = c(HB1 = 20, TRANSF_PLT100 = 2.5, BLAST5 = 0, CYTOVEC = 0, TP53multi = 0,
    FLT3 = 0, MLL_PTD = 0, SF3B1_5q = 0, NPM1 = 0, RUNX1 = 0, NRAS = 0, ETV6 = 0, IDH2 =
    0, CBL = 0, EZH2 = 0, U2AF1 = 0, SRSF2 = 0, DNMT3A = 0, ASXL1 = 0, KRAS = 0,
    SF3B1_alpha = 1),
  worstValues = c(HB1 = 4, TRANSF_PLT100 = 0, BLAST5 = 4, CYTOVEC = 4, TP53multi = 1,
    FLT3 = 1, MLL_PTD = 1, SF3B1_5q = 1, NPM1 = 1, RUNX1 = 1, NRAS = 1, ETV6 = 1, IDH2 =
    1, CBL = 1, EZH2 = 1, U2AF1 = 1, SRSF2 = 1, DNMT3A = 1, ASXL1 = 1, KRAS = 1,
    SF3B1_alpha = 0),
  rounding = TRUE,
  rounding.digits = 2,
  risk.cutpoints = c(-1.5, -0.5, 0, 0.5, 1.5),
  risk.cat = c("Very Low", "Low", "Moderate Low", "Moderate High", "High", "Very High"),
  range.max = 1
)

Arguments

path.file	path to the input data file. Allowed formats are .csv, .tsv, .xls, and .xlsx.
sheet	sheet number for excel format input file. Default is 1.
genesRes	a vector containing the names of the residual genes. Default is from the IPSS-M publised model.
Nref	the average reference value for min(Nres,2) where Nres is the number of mutated residual genes.
betaValues	a covariate vector of the model weights. Should have name attributes.
meanValues	vector of average values for each covariate. Should have the same names attributes as in betaValues.
bestValues	vector of best values (leading to minimal risk) for each covariate (nRes2 not needed as already taken care of in IPSSMprocess).
worstValues	vector of worst values (leading to maximal risk) for each covariate (nRes2 not needed as already taken care of in IPSSMprocess).
rounding	should the raw IPSS-M risk score be rounded. Default is TRUE.
rounding.digits	number of digits for the rounding. Default is 2.
risk.cutpoints	cutpoints to be applied to the IPSS-M risk score to create risk categories.
risk.cat	names of the IPSS-M risk categories.
range.max	threshold for the allowed maximal range in IPSS-M risk (worst - best) to confidently report the mean scenario as the main result. Default 1.

Value

A patient annoated results data.frame.

Examples

path.file <- system.file("extdata", "IPSSMexample.csv", package = "ipssm")
ddres <- IPSSMwrapper(path.file)
print(ddres)

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