genefu (version 2.4.2)

ihc4: Function to compute the IHC4 prognostic score as published by Paik et al. in 2004.

Description

This function computes the prognostic score based on four measured IHC markers (ER, PGR, HER2, Ki-67), following the algorithm as published by Cuzick et al. 2011. The user has the option to either obtain just the shrinkage-adjusted IHC4 score (IHC4) or the overall score htat also combines the clinical score (IHC4+C)

Usage

ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithClinical=FALSE, na.rm = FALSE)

Arguments

ER

ER score between 0-10, calculated as (H-score/30)

PGR

Progesterone Receptor score between 0-10

HER2

Her2/neu status (0 or 1).

Ki67

Ki67 score based on percentage of positively staining malignant cells

age

patient age

size

tumor size in cm.

grade

Histological grade, i.e. low (1), intermediate (2) and high (3) grade.

node

Nodal status.

ana

treatment with anastrozole

scoreWithClinical

TRUE to get IHC4+C score, FALSE to get just the IHC4 score.

na.rm

TRUE if missing values should be removed, FALSE otherwise.

Value

• Shrinkage-adjusted IHC4 score or the Overall Prognostic Score based on IHC4+C (IHC4+Clinical Score)

References

Jack Cuzick, Mitch Dowsett, Silvia Pineda, Christopher Wale, Janine Salter, Emma Quinn, Lila Zabaglo, Elizabeth Mallon, Andrew R. Green, Ian O. Ellis, Anthony Howell, Aman U. Buzdar, and John F. Forbes (2011) "Prognostic Value of a Combined Estrogen Receptor, Progesterone Receptor, Ki-67, and Human Epidermal Growth Factor Receptor 2 Immunohistochemical Score and Comparison with the Genomic Health Recurrence Score in Early Breast Cancer", Journal of Clinical Oncologoy, 29(32):4273--4278.

Examples

## load NKI dataset
data(nkis)
## compute shrinkage-adjusted IHC4 score
count<-nrow(demo.nkis)
ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1:10, size=count,replace=TRUE),
HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100, size=count,replace=TRUE),
scoreWithClinical=FALSE, na.rm=TRUE)

## compute IHC4+C score
ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1:10, size=count,replace=TRUE),
HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100, size=count,replace=TRUE),
age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis[ ,"grade"],node=demo.nkis[ ,"node"],
ana=sample(x=0:1,size=count,replace=TRUE), scoreWithClinical=TRUE, na.rm=TRUE)