Description Usage Arguments Value See Also Examples
Starting with the default value of mtry, search for the optimal value (with respect to OutofBag error estimate) of mtry for snpRF.
1 2 3 
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 Xchromosome, 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

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 
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
.
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)

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