setGeneric("count.unknowns", function(object) standardGeneric("count.unknowns"))
setMethod("count.unknowns","GENOME",function(object){
region.names <- object@region.names
n.region.names <- length(region.names)
if(object@big.data){region.names <- NULL} # because of memory space
npops <- length(object@populations) # N Populations
#########################################
# INIT
#########################################
nam <- paste("pop",1:npops)
init1 <- matrix(0,n.region.names,npops)
missing.nucleotides <- init1
missing.frequencies <- vector("list",n.region.names) # region stats
change <- object@region.stats
#--------------------------------------------------
# Names ----------------------------------------
rownames(missing.nucleotides) <- region.names
colnames(missing.nucleotides) <- nam
# ----------------------------------------------
## PROGRESS #########################
progr <- progressBar()
#####################################
for(xx in 1:n.region.names){
### if Subsites ----------------------------------
bial <- popGetBial(object,xx)
if(length(bial)!=0){ # if a biallelic position exists
populations <- object@region.data@populations[[xx]] # Pop
if(length(object@region.data@popmissing[[xx]])!=0){popmissing <- object@region.data@popmissing[[xx]];respop <- (1:npops)[-popmissing]}else{respop <- 1:npops}
res <- calc_miss(bial,populations)
# fill detailed Slots --------------------------------#
missing.frequencies[[xx]] <- res$miss.freq
# ----------------------------------------------------#
missing.nucleotides[xx,respop] <- res$miss.nuc
# PROGRESS #######################################################
progr <- progressBar(xx,n.region.names, progr)
###################################################################
}
}
change@missing.freqs <- missing.frequencies
object@region.stats <- change
rm(change)
gc()
object@missing.freqs <- missing.nucleotides
return(object)
})
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