npi: Function to compute the Nottingham Prognostic Index

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Function to compute the Nottingham Prognostic Index

Description

This function computes the Nottingham Prognostic Index (NPI) as published in Galeat et al, 1992. NPI is a clinical index shown to be highly prognostic in breast cancer.

Usage

npi(size, grade, node, na.rm = FALSE)

Arguments

size	tumor size in cm.
grade	Histological grade, i.e. low (1), intermediate (2) and high (3) grade.
node	Nodal status. If only binary nodal status (0/1) is available, map 0 to 1 and 1 to 3.
na.rm	TRUE if missing values should be removed, FALSE otherwise.

Details

The risk prediction is either Good if score < 3.4, Intermediate if 3.4 <= score <- 5.4, or Poor if score > 5.4.

Value

A list with items:

• score: Continuous signature scores

• risk: Binary risk classification, 1 being high risk and 0 being low risk.

References

Galea MH, Blamey RW, Elston CE, and Ellis IO (1992) "The nottingham prognostic index in primary breast cancer", Breast Cancer Reasearch and Treatment, 22(3):207-219.

See Also

st.gallen

Examples

# load NKI dataset
data(nkis)
# compute NPI score and risk classification
npi(size=demo.nkis[ ,"size"], grade=demo.nkis[ ,"grade"],
  node=ifelse(demo.nkis[ ,"node"] == 0, 1, 3), na.rm=TRUE)

bhklab/genefu documentation built on June 2, 2022, 2:56 p.m.