Nothing
f.sep.data <- function( data, info ){
##
## RESHAPE GENETIC DATA INTO COMPLETE HAPLOTYPE DATA
##
design <- info$model$design
xchrom <- info$model$xchrom
n.vars <- info$filespecs$n.vars
alleles <- info$haplos$alleles
nloci <- length( alleles )
# checking whether any locus contain only one allele
# (this can happen if we omit some data, e.g., due to missingness);
# if so, re-code this data
for(i in 1:nloci){
alleles.count <- length( alleles[[ i ]] )
if( alleles.count == 1 ){
if(design %in% c("triad", "cc.triad")){
chosen.cols <- ((i-1)*6 + 1):((i-1)*6 + 6)
}
if(design == "cc"){
chosen.cols <- ((i-1)*2 + 1):((i-1)*2 + 2)
}
data$gen.data[ ,chosen.cols ] <- 1
}
}
## TEST FOR HWE
if(!xchrom){
.HWE.res <- f.HWE.design( data, design = design )
} else {
.HWE.res <- f.HWE.design( data, design = design, sex = data$cov.data[, info$variables$sex] )
}
## RESHAPE GENETIC DATA
if( xchrom ){
.data.gen <- f.sort.alleles.new( data, design = design, xchrom = T, sex = data$cov.data[, info$variables$sex] )
} else {
.data.gen <- f.sort.alleles.new( data, design = design )
}
return( list(data.gen = .data.gen, HWE.res = .HWE.res) )
}
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