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# FREGAT (c) 2016 Gulnara R. Svishcheva & Nadezhda M. Belonogova, ICG SB RAS
check.spec.famSKAT <- function() {
method <- check.method(method)
kernel <- match.arg(kernel, c('linear.weighted', 'quadratic', 'IBS', 'IBS.weighted', '2wayIX'))
if (length(rho) > 1 | (length(rho) == 1 & rho)) {
rhos <- check.rho(rho, kernel)
rho <- TRUE
return.variance.explained <- FALSE
sapply(c('fweights', 'weights', 'method', 'kernel', 'rhos', 'rho', 'return.variance.explained'),
function(x) get(x), simplify = FALSE, USE.NAMES = TRUE)
} else {
rho <- FALSE
sapply(c('fweights', 'weights', 'method', 'kernel', 'rho'),
function(x) get(x), simplify = FALSE, USE.NAMES = TRUE)
}
}
check.spec.famFLM <- function() {
stat <- match.arg(stat, c('F', 'Chisq', 'LRT'))
BSF <- match.arg(BSF, c('fourier', 'bspline'))
if (gtype < 3) {
if (is.null(positions)) stop("'positions' are missing, with no default")
if (length(positions) != k) stop("Dimensions of 'positions' and 'genodata' do not match")
}
g <- TRUE
# if (missing(GVF)) g <- FALSE
if (is.null(GVF)) g <- FALSE
if (is.logical(GVF)){
if (!GVF) g <- FALSE else GVF <- 'bspline'
}
if (g) GVF <- match.arg(GVF, c('fourier', 'bspline'))
kb0 <- kg0 <- order0 <- FALSE
if (BSF == 'bspline') {
order0 <- check.basis(order, 'order')
kb0 <- check.basis(kb, 'basis', 'bspline', order0)
} else { kb0 <- check.basis(kb, 'basis', 'fourier') }
if (g) {
if (GVF == 'bspline') {
if (!order0) order0 <- check.basis(order, 'order')
kg0 <- check.basis(kg, 'basis', 'bspline', order0)
} else { kg0 <- check.basis(kg, 'basis', 'fourier') }
}
# base condition is kg >= kb
if (g) {
if (kg0 < kb0) {
kb0 <- kg0
warning (paste('kb cannot exceed kg, kb set to', kg0))
}
if (kg0 == kb0) {
g <- FALSE
if (GVF == 'bspline' & BSF == 'fourier') BSF <- 'bspline'
if (GVF == 'fourier' & BSF == 'bspline') BSF <- 'fourier'
warning ("GVF has no effect under kg = kb, the equivalent model with '", BSF, "' for BSF will be used")
}
}
# if g then kg > kb
# if kg == kb then !g
if (BSF == 'bspline') betabasis0 = create.bspline.basis(norder = order0, nbasis = kb0)
else betabasis0 <- create.fourier.basis(c(0, 1), nbasis = kb0)
if (g) {
if (GVF == 'bspline') { genobasis0 <- create.bspline.basis(norder = order0, nbasis = kg0)
} else { genobasis0 <- create.fourier.basis(c(0, 1), nbasis = kg0) }
J0 <- inprod(genobasis0, betabasis0)
model0 <- paste(GVF, kg0, '-', BSF, kb0, sep = '')
}
else model0 <- paste(0, '-', BSF, kb0, sep = '')
# all fourier bases are odd
omit.linear.dependent <- TRUE
if (g) sapply(c('stat', 'BSF', 'g', 'GVF', 'kb0', 'kg0', 'order0', 'model0', 'genobasis0', 'betabasis0', 'J0', 'omit.linear.dependent'),
function(x) get(x), simplify = FALSE, USE.NAMES = TRUE)
else sapply(c('stat', 'BSF', 'g', 'kb0', 'order0', 'model0', 'betabasis0', 'omit.linear.dependent'),
function(x) get(x), simplify = FALSE, USE.NAMES = TRUE)
}
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