Nothing
setGeneric("region.as.fasta", function(object, region.id= FALSE, filename = FALSE, type=1, ref.chr=FALSE) standardGeneric("region.as.fasta"))
setMethod("region.as.fasta", "GENOME",
function(object,region.id,filename,type,ref.chr){
if(region.id[1]==FALSE){
stop("Define a region !")
}
if(type==1){
bial <- popGetBial(object,region.id)
subst <- object@region.data@biallelic.substitutions[[region.id]]
minor <- subst[1,]
mayor <- subst[2,]
for(xx in 1:dim(bial)[2]){
vek <- bial[,xx]
ids.minor <- vek==1
ids.mayor <- vek==0
bial[ids.minor,xx] <- minor[xx]
bial[ids.mayor,xx] <- mayor[xx]
}
number <- c(1,1,1,1,2,2,3,3,4,4,5,5,5,6)
nuc <- c("T","t","U","u","C","c","G","g","A","a","N","n","?","-")
bial <- apply(bial,1,function(x){return(nuc[match(x,number)])})
bial <- t(bial)
APE_write.dna(bial,file=filename,colsep="",format="fasta") # This function is from the APE package on CRAN
return(bial)
}
if(type==2){
# Init whole MATRIX
## Reading the reference chromosome
file.info <- .Call("get_dim_fasta",ref.chr)
CHR <- .Call("get_ind_fasta",ref.chr,1,file.info[[1]][2])
bial.sites <- object@region.data@biallelic.sites[[region.id]]
s_tart <- bial.sites[1]
e_end <- bial.sites[length(bial.sites)]
bial <- popGetBial(object,region.id)
FILLnuc <- CHR[s_tart:e_end]
# whole Matrix
RETMAT <- matrix(rep(FILLnuc,dim(bial)[1]),nrow=dim(bial)[1],ncol=length(FILLnuc),byrow=TRUE)
subst <- object@region.data@biallelic.substitutions[[region.id]]
minor <- subst[1,]
mayor <- subst[2,]
# fill the SNPS
for(xx in 1:dim(bial)[2]){
vek <- bial[,xx]
ids.minor <- vek==1
ids.mayor <- vek==0
bial[ids.minor,xx] <- minor[xx]
bial[ids.mayor,xx] <- mayor[xx]
}
number <- c(1,1,1,1,2,2,3,3,4,4,5,5,5,6)
nuc <- c("T","t","U","u","C","c","G","g","A","a","N","n","?","-")
bial <- apply(bial,1,function(x){return(nuc[match(x,number)])})
bial <- t(bial)
ind.names <- rownames(bial)
RETMAT <- apply(RETMAT,1,function(x){return(nuc[match(x,number)])})
RETMAT <- t(RETMAT)
fillids <- match(bial.sites,s_tart:e_end)
RETMAT[,fillids] <- bial
rownames(RETMAT) <- ind.names
# if a region is specified via splitting.data concatenate left and right-hand nucleotides
if( length(grep("-",object@region.names[region.id]))!=0 ){
leftrightPOS <- as.numeric(strsplit(object@region.names[region.id]," - ")[[1]])
leftPOS <- leftrightPOS[1]
rightPOS <- leftrightPOS[2]
# s_tart
# ---------------------------------------------------------------------------------
# left hand matrix
leftRegion <- leftPOS:(s_tart-1)
leftNUCS <- CHR[leftRegion]
# convert to character
leftNUCS <- nuc[match(leftNUCS,number)]
leftNUCS <- rep(leftNUCS,length(ind.names))
leftNUCS <- matrix(leftNUCS,nrow=length(ind.names),ncol=length(leftRegion),byrow=TRUE)
#e_end
# ----------------------------------------------------------------------------------
# right hand matrix
rightRegion <- (e_end+1):rightPOS
rightNUCS <- CHR[rightRegion]
# convert to character
rightNUCS <- nuc[match(rightNUCS,number)]
rightNUCS <- rep(rightNUCS,length(ind.names))
rightNUCS <- matrix(rightNUCS,nrow=length(ind.names),ncol=length(rightRegion),byrow=TRUE)
# concatenate matrices
RETMAT <- cbind(leftNUCS,RETMAT,rightNUCS)
}
APE_write.dna(RETMAT,file=filename,colsep="",format="fasta") # This function is from the ape package on CRAN
return(RETMAT)
}
})# End of function
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