npi: Function to compute the Nottingham Prognostic Index

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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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

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## 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)

genefu documentation built on May 31, 2017, 2:56 p.m.

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