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## biom.options.R: modeled after pls.options.R.
## New version August 4, 2014. (Thanks for the example BH!)
## The list of initial options, for the moment all pertaining to
## stability-based biomarkers selection
## 21-11-2011: added "lasso" as possibility for fmethods. We assume
## that the number of observations is smaller than the number of
## variables. Eventually we also take lasso to be an empty list. Let's see.
biom.options <- function(..., reset = FALSE) {
if (reset) {
.biom.Options$options <-
list(max.seg = 100, oob.size = NULL, oob.fraction = .3,
variable.fraction = .5, ntop = 10, min.present = .1,
fmethods = c("studentt", "shrinkt", "pcr", "pls", "vip", "lasso"),
univ.methods = c("studentt", "shrinkt"),
lasso = list(alpha = 1, nlambda = 100),
nset = 10000, HCalpha = .1)
.biom.Options$options
}
temp <- list(...)
if (length(temp) == 0)
.biom.Options$options
current <- .biom.Options$options
if (length(temp) == 1 && is.null(names(temp))) {
arg <- temp[[1]]
switch(mode(arg),
list = temp <- arg,
character = return(.biom.Options$options[arg]),
stop("invalid argument: ", sQuote(arg)))
}
if (length(temp) == 0) return(current)
n <- names(temp)
if (is.null(n)) stop("options must be given by name")
changed <- current[n]
current[n] <- temp
.biom.Options$options <- current
invisible(current)
}
.biom.Options <- new.env(parent = emptyenv())
biom.options(reset = TRUE)
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