ihc4: Function to compute the IHC4 prognostic score as published by...

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

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)

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.