#' create a matrix from pairwise data
#'
#'
#' @param snpcov pairwise covariance matrix
#' @param snps a vector of snps to subset
#'
#' @export
create.snpcov.matrix <- function(snpcov){
snpcov <- snpcov[!is.na(VALUE)]
snpcov.dup <- snpcov
snpcov.dup$RSID1 <- snpcov$RSID2
snpcov.dup$RSID2 <- snpcov$RSID1
snpcov <- rbind(snpcov,snpcov.dup)
##to matrix
snpcov.mat <- reshape(snpcov,idvar="RSID1",timevar = "RSID2", direction="wide")
names(snpcov.mat) <- gsub("VALUE.","",names(snpcov.mat))
snp.ids <- snpcov.mat$RSID1
snpcov.mat <- snpcov.mat[,-1]
snpcov.mat <- sapply(snpcov.mat,as.numeric)
snpcov.mat <- as.matrix(snpcov.mat)
rownames(snpcov.mat) <- snp.ids
snpcov.mat <- snpcov.mat[,snp.ids]
return(snpcov.mat)
}
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