npi {genefu} | R Documentation |
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.
npi(size, grade, node, na.rm = FALSE)
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 |
na.rm |
|
The risk prediction is either Good
if score < 3.4, Intermediate
if 3.4 <= score <- 5.4, or Poor
if score > 5.4.
score |
Continuous signature scores |
risk |
Binary risk classification, |
Benjamin Haibe-Kains
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.
## 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)