#' @title plsda from mixOmics, credit to mixOmics team
#' @param X mass_dataset or matrix
#' @param ... Other parameters
#' @export
setGeneric(
name = "plsda",
def = function(X, ...)
standardGeneric("plsda")
)
#' @title plsda
#' @method plsda mass_dataset
#' @param X mass_dataset
#' @param Y a factor or a class vector for the discrete outcome.
#' @param ncomp ncomp
#' @param scale scale
#' @param tol tol
#' @param max.iter max.iter
#' @param near.zero.var near.zero.var
#' @param logratio logratio
#' @param multilevel multilevel
#' @param all.outputs all.outputs
#' @export
#' @rdname multivariate-mass_dataset
#' @importFrom mixOmics plsda plotIndiv plotVar
#' @return A plsda class
setMethod(f = "plsda",
signature(X = "mass_dataset"),
function (X,
Y = NULL,
ncomp = 2,
scale = FALSE,
tol = 1e-06,
max.iter = 100,
near.zero.var = FALSE,
logratio = "none",
multilevel = NULL,
all.outputs = TRUE) {
expression_data = X@expression_data
linn.pls <-
mixOmics::plsda(
X = as.matrix(t(expression_data)),
Y = Y,
ncomp = ncomp,
scale = FALSE,
tol = tol,
max.iter = max.iter,
near.zero.var = near.zero.var,
logratio = logratio,
multilevel = multilevel,
all.outputs = all.outputs
)
return(linn.pls)
})
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