tuneSnpRF: Tune snpRF for the optimal mtry parameter

Description Usage Arguments Value See Also Examples

View source: R/tuneSnpRF.R

Description

Starting with the default value of mtry, search for the optimal value (with respect to Out-of-Bag error estimate) of mtry for snpRF.

Usage

1
2
3
tuneSnpRF(x.autosome=NULL, x.xchrom=NULL, xchrom.names=NULL, x.covar=NULL, y, 
          mtryStart, ntreeTry=50, stepFactor=2, improve=0.05, trace=TRUE, 
          plot=TRUE, doBest=FALSE, ...)

Arguments

x.autosome

A matrix of autosomal markers with each column correspond to a SNP coded as count of a particular allele (i.e. 0,1 or 2), and each row corresponding to a sample/individual.

x.xchrom

A matrix of X chromosome markers, each marker coded as two adjacent columns, alleles of a marker are coded as 0 or 1 for carrying a particular allele. Although males only have one X-chromosome, their markers are coded as 2 columns as well, the second column being a duplicate of the first. Each row of this matrix corresponds to a sample/individual. This data must be phased in chromosomal order.

xchrom.names

A vector of names for markers (1 name per marker) in the x.xchrom matrix ordered in the same manner as markers in x.xchrom.

x.covar

A matrix of covariates, each column being a different covariate and each row, a sample/individual.

y

A response vector. Must be a factor, regression has not been implemented.

mtryStart

starting value of mtry; default is the same as in snpRF

ntreeTry

number of trees used at the tuning step

stepFactor

at each iteration, mtry is inflated (or deflated) by this value

improve

the (relative) improvement in OOB error must be by this much for the search to continue

trace

whether to print the progress of the search

plot

whether to plot the OOB error as function of mtry

doBest

whether to run a forest using the optimal mtry found

...

options to be given to snpRF

Value

If doBest=FALSE (default), it returns a matrix whose first column contains the mtry values searched, and the second column the corresponding OOB error.

If doBest=TRUE, it returns the snpRF object produced with the optimal mtry.

See Also

snpRF

Examples

1
2
3
4
data(snpRFexample)
eg.res <- tuneSnpRF(x.autosome=autosome.snps,x.xchrom=xchrom.snps,
                    xchrom.names=xchrom.snps.names,x.covar=covariates, 
                    y=phenotype, stepFactor=1.5)

snpRF documentation built on May 29, 2017, 8:36 p.m.

Related to tuneSnpRF in snpRF...