Nothing
#
# y.all :
# for only intercept, set "intercept"
Meta_Null_Model<-function(y.list, x.list, n.cohort, out_type="C", n.Resampling=0 ){
re<-list()
re$n.g=n.cohort
re$out<-list()
re$ID<-list()
re$n.each<-rep(0,n.cohort)
re$out_type=out_type
count<-1
n.x = length(x.list)
for(i in 1:n.cohort){
y = y.list[[i]]
X = x.list[[i]]
if(is.vector(X)){
if(X[1] == "intercept"){
formula = y ~ 1
} else if( length(X) == 1 && is.character(X)){
msg<-sprintf("ERROR: %d element of x.list is wrong. For intercept-only, it should be \"intercept\".",i)
stop(msg)
} else {
formula = y ~ X
}
} else {
formula = y ~ X
}
re$out[[i]]<-SKAT_Null_Model(formula, out_type=out_type, Adjustment=FALSE, n.Resampling=n.Resampling)
if(length(re$out[[i]]$id_include) != length(y)){
msg<-sprintf("Missing values in cohort %d. The current version cannot handle missing values in either phenotypes or covariates!",i)
stop(msg)
}
n1<-length(re$out[[i]]$res)
re$ID[[i]]<-count:(count +n1-1)
count<-count + n1
re$n.each[i]<-n1
}
class(re)<-"META_NULL_Model"
return(re)
}
#
# y.all :
# for only intercept, set "intercept"
Meta_Null_Model_EmmaX<-function(y.list, x.list, n.cohort, K.list=NULL, Kin.File.list=NULL){
#require(SKATEmmaX)
re<-list()
re$n.g=n.cohort
re$out<-list()
re$ID<-list()
re$n.each<-rep(0,n.cohort)
re$out_type="K"
count<-1
n.x = length(x.list)
for(i in 1:n.cohort){
y = y.list[[i]]
X = x.list[[i]]
if(is.vector(X)){
if(X[1] == "intercept"){
formula = y ~ 1
} else if( length(X) == 1 && is.character(X)){
msg<-sprintf("ERROR: %d element of x.list is wrong. For intercept-only, it should be \"intercept\".",i)
stop(msg)
} else {
formula = y ~ X
}
} else {
formula = y ~ X
}
if(!is.null(K.list)){
re$out[[i]]<-SKAT_NULL_emmaX(formula, K=K.list[[i]])
} else if(!is.null(Kin.File.list)){
re$out[[i]]<-SKAT_NULL_emmaX(formula, Kin.File=Kin.File.list[[i]])
} else {
stop("Either K.list or Kin.File.list should have non-null value!")
}
if(length(re$out[[i]]$id_include) != length(y)){
msg<-sprintf("Missing values in cohort %d. The current version cannot handle missing values in either phenotypes or covariates!",i)
stop(msg)
}
n1<-length(re$out[[i]]$res)
re$ID[[i]]<-count:(count +n1-1)
count<-count + n1
re$n.each[i]<-n1
}
class(re)<-"META_NULL_Model_EmmaX"
return(re)
}
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