ihc4 {genefu} | R Documentation

## 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)

[Package genefu version 2.26.0 Index]