npi {genefu} | R Documentation

## 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

`score` | Continuous signature scores
`risk` | Binary risk classification, `1` being high risk and `0` being low risk.

### Author(s)

Benjamin Haibe-Kains

### 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)

[Package genefu version 2.12.0 Index]