README.md

ipssm

R Package for the Molecular International Prognostic Scoring System (IPSS-M) for Myelodysplastic Syndromes.

🚀 Installation instructions

# install devtools if you don't have it already for easy installation
# install.packages("devtools")
library(devtools)
install_github("papaemmelab/ipssm",ref = "main")

💥 Usage

The worflow below consists of 4 simple steps, namely 1) Read your input data file and perform some validation on the data, 2) Process the variables in a suitable format for the model, 3) Calculate the IPSS-M risk score and risk category (under the best, mean, and worst scenario to account for missing data if there are some), 4) Annotate the results.

# load the ipssm library
library("ipssm")
# path to your input data file
path.file <- system.file("extdata", "IPSSMexample.csv", package = "ipssm")
#path.file <- system.file("extdata", "IPSSMexample.xlsx", package = "ipssm") # equivalent

# 1) Read and Validate File
dd <- IPSSMread(path.file)

# 2) Process User Input Variables into Model Variables
dd.process <- IPSSMprocess(dd)

# 3) Calculate IPSS-M
dd.res <- IPSSMmain(dd.process)

# 4) Annotate Results
dd.annot <- IPSSMannotate(dd.res)

Alternatively the above steps can be performed with a one-line code using a wrapper function, as follows.

# load the ipssm library
library("ipssm")
# path to your input data file
path.file <- system.file("extdata", "IPSSMexample.csv", package = "ipssm")

# call the IPSS-M wrapper function
ddall <- IPSSMwrapper(path.file)

📃 Reference

Bernard E, Tuechler H, Greenberg PL, Hasserjian RP, Arango Ossa JE et al. Molecular International Prognostic Scoring System for Myelodysplastic Syndromes, NEJM Evidence 2022.

🍀 Other

In addition to the R package, you may be interested in checking out our Online Web Calculator with Juan E Arango Ossa as main developer.

❓ Question

Any questions feel free to contact ElsaB.