Description Usage Arguments Value See Also Examples
Starting with the default value of mtry, search for the optimal value (with respect to Out-of-Bag 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 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
|
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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