#' Annotate Wolbachia positions
#'
#' By using a bed file each position of Wolbahcia is annotated
#' @author Elves H Duarte
#' @param x A list of positions to be annotated.
#' @return Retur a list of genes (or not) of Wolbachia locus.
#' @export
pos2gene=function(x)
{
data("wolb_genes")
.chr=1:1268079
{
if(length(x)==1)
{
##
if(x %in% .chr)
{
gen=subset(.genes, .genes$V5>=x)[1,]
exon=gen$V4:gen$V5
if(x %in% exon)
gene_list=as.character(gen[1,6])
else
gene_list="non-coding"
}
else
{
gene_list=NA
}
}
else
{
gene_list=NULL
for(n in 1:length(x))
{
if(x[n] %in% .chr)
{
gen=subset(.genes, .genes$V5>=x[n])[1,]
exon=gen$V4:gen$V5
if(x[n] %in% exon)
gene_list[n]=as.character(gen[1,6])
else
gene_list[n]="non-coding"
}
else
{
gene_list[n]=NA
}
}
}
}
return(gene_list)
}
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