Nothing
validate.setup <- function(setup){
if(is.character(setup)){ # path of setup file
ld <- try(load(setup), silent = TRUE)
if(error.try(ld)){
msg <- paste('Cannot load', setup)
stop(msg)
}
}
if(!is.list(setup)){
msg <- 'setup should be a list'
stop(msg)
}
if(!all(c('norm.stat', 'options') %in% names(setup))){
msg <- 'norm.stat or options is not found in setup'
stop(msg)
}
for(i in 1:length(setup$norm.stat$V)){
rs <- sort(names(setup$norm.stat$score0[[i]]))
if(length(rs) == 1){
# the chromosome contains only one SNP.
# in that case, setup$norm.stat$V[[i]] might not be a matrix if version between v0.8.10 and v0.8.14 was used
# we need to reformat it as a 1x1 matrix, and also add row/column names to it
setup$norm.stat$V[[i]] <- matrix(setup$norm.stat$V[[i]], dimnames = list(rs, rs))
}else{
setup$norm.stat$score0[[i]] <- setup$norm.stat$score0[[i]][rs]
setup$norm.stat$V[[i]] <- setup$norm.stat$V[[i]][rs, rs, drop = FALSE]
}
}
setup$options$only.setup <- NULL
setup$options$save.setup <- NULL
setup$options$path.setup <- NULL
setup
}
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