resampling.cv: Resampling to find the optimal number of markers

In agricolae: Statistical Procedures for Agricultural Research

Resampling to find the optimal number of markers

Description

This process finds the curve of CV for a different number of markers which allows us to determine the number of optimal markers for a given relative variability. A method of the curvature.

Usage

resampling.cv(A, size, npoints)

Arguments

A	data frame or matrix of binary data
size	number of re-samplings
npoints	Number of points to consider the model

Value

lm(formula = CV ~ I(1/marker))
Table with variation coefficient by number of markers

Author(s)

Felipe de Mendiburu

References

Efron, B., Tibshirani, R. (1993) An Introduction to the Boostrap. Chapman and Hall/CRC

See Also

cv.similarity, similarity

Examples

library(agricolae)
#example table of molecular markers
data(markers)
study<-resampling.cv(markers,size=1,npoints=15)
#
# Results of the model
summary(study$model)
coef<-coef(study$model)
py<-predict(study$model)
Rsq<-summary(study$model)$"r.squared"
table.cv <- data.frame(study$table.cv,estimate=py)
print(table.cv)

# Plot CV
#startgraph
limy<-max(table.cv[,2])+10
plot(table.cv[,c(1,2)],col="red",frame=FALSE,xlab="number of markers",
ylim=c(10,limy), ylab="CV",cex.main=0.8,main="Estimation of the number of markers")
ty<-quantile(table.cv[,2],1)
tx<-median(table.cv[,1])
tz<-quantile(table.cv[,2],0.95)
text(tx,ty, cex=0.8,as.expression(substitute(CV == a + frac(b,markers),
list(a=round(coef[1],2),b=round(coef[2],2)))) )
text(tx,tz,cex=0.8,as.expression(substitute(R^2==r,list(r=round(Rsq,3)))))

# Plot CV = a + b/n.markers
fy<-function(x,a,b) a+b/x
x<-seq(2,max(table.cv[,1]),length=50)
y <- coef[1] + coef[2]/x
lines(x,y,col="blue")
#grid(col="brown")
rug(table.cv[,1])
#endgraph

agricolae documentation built on Oct. 23, 2023, 1:06 a.m.