R/correctness.R:
BIOC
TRONCO: TRONCO, an R package for TRanslational ONCOlogy
#' is.compliant(test_dataset)
#'
#' @param x A TRONCO compliant dataset.
#' is.compliant(test_dataset)
#'
#' @param x A TRONCO compliant dataset.
= NULL,
beta0 = -0.5, beta = 1.5, maf = 0.25, sample.y = TRUE, p.cutoff = 0.5,
err.fun = NULL, rand = NA
= c("mean", "median"), err.fun = c("sd", "sem", "var",
"ci"), ci = 0.95, num.bootstraps = 1, boot.err.mode = 1
err.fun = "[ERR]",
stage = !(all(is.null(x$stages)) || all(is.na(x$stages)))
Arguments
")){
if(type[1] %in% c("mse", "mspe")){
err.fun <- function(tsb) {
= function(e) NULL)
err.funs = which(!(funs %in% names(fun.list)))
if (length(err.funs) > 0L)
# --
if(has.g2) {
aggr.res.x <- aplot.statErr(x[idx], fun=aggr.fun, err.fun=aggr.err.fun,
=TRUE,p.cutoff=0.5,err.fun=NULL,rand=NA,...){
check.snplist<-TRUE
if(is.null(list.snp) & is.null(list.ia
`getCall` <-
function(call,n.obs){
fun<-as.character(call$err.fun)
), function(x) order(x, decreasing = FALSE))
znn <- data.frame(z)
z <- lapply(data.frame(D), function
. It now forces interpolation with NN.
if (nnas > 0)
nn <- knnidw(1, rmax = .Machine$double.xmax)
("stepwise.eval.stud.expr")
if (!is.null(seed))
set.seed(seed)
silent = FALSE) {
is.compliant(x, err.fun='events.selection: input')
dataset = x$genotypes
("stepwise.eval.stud.expr")
if (!is.null(seed))
set.seed(seed)
<- zu[1:2]
znn <- zu[(l-1):l]
} else {
type <- attr(x, "entry")
key <- attr(x, "key")
y <- as.list(x)
= .Machine$double.xmax)
sub_grid <- data.frame(X = grid$X[isna], Y = grid$Y[isna])
znn <- nn(ground, sub_grid)
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