Nothing
# slot p
setGeneric('p', function(x) standardGeneric('p'), package="gaston")
setMethod('p', signature = 'bed.matrix', def = function(x) x@p)
setGeneric('p<-', function(x,value) standardGeneric('p<-'), package="gaston")
setReplaceMethod('p', 'bed.matrix', function(x,value) {
if(length(value) != ncol(x)) stop("dimensions mismatch")
x@p <- value;
x} )
# slot mu
setGeneric('mu', function(x) standardGeneric('mu'), package="gaston")
setMethod('mu', signature = 'bed.matrix', def = function(x) x@mu)
setGeneric('mu<-', function(x,value) standardGeneric('mu<-'), package="gaston")
setReplaceMethod('mu', 'bed.matrix', function(x,value) {
if(length(value) != ncol(x)) stop("dimensions mismatch")
x@mu <- value;
x} )
# slot sigma
setGeneric('sigma', function(x) standardGeneric('sigma'), package="gaston")
setMethod('sigma', signature = 'bed.matrix', def = function(x) x@sigma)
setGeneric('sigma<-', function(x,value) standardGeneric('sigma<-'), package="gaston")
setReplaceMethod('sigma', 'bed.matrix', function(x,value) {
if(length(sigma) != ncol(x)) stop("dimensions mismatch")
x@sigma <- value;
x} )
# center_scale
setGeneric('standardize', function(x) standardGeneric('standardize'), package="gaston")
setMethod('standardize', signature = 'bed.matrix',
def = function(x) if(x@standardize_p) "p" else if(x@standardize_mu_sigma) "mu_sigma" else "none"
)
setGeneric('standardize<-', function(x,value) standardGeneric('standardize<-'), package="gaston")
setReplaceMethod('standardize', 'bed.matrix', function(x,value=c("p","mu_sigma","none")) {
switch(match.arg(value),
p = { if(length(x@p) != ncol(x))
stop("x@p must be defined and have the appropriate length");
x@standardize_p <- TRUE; x@standardize_mu_sigma <- FALSE;
} ,
mu_sigma = { if(length(x@mu) != ncol(x) | length(x@sigma) != ncol(x))
stop("x@mu and x@sigma must be defined and have the appropriate length");
x@standardize_p <- FALSE; x@standardize_mu_sigma <- TRUE;
} ,
none = {x@standardize_p <- FALSE; x@standardize_mu_sigma <- FALSE;}
);
x } )
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