Nothing

```
#' convert a VCF into an 012,-1 matrix and read_depth bin matrix for estimation
#'
#' @param v a vcfR object into which a VCF file has been read
#' @param DF Field to use for obtaining total read depth. Currently
#' all that is available is DP.
#' @param minBin minimum number of observations for each read depth bin
#' @return This sends back a list with \code{mat012}: the 012,-1 matrix of genotypes, and
#' \code{dp_bins_list}: the list returned by bin_depths().
#' @export
#' @keywords internal
#' @examples
#' pv <- prep_vcf_for_est_m_rd(lobster_buz_2000, minBin = 1000)
prep_vcf_for_est_m_rd <- function(v, DF = "DP", minBin) {
# check to make sure the field named in DF exists.
#vt <- vcfR2tidy(v, info_only = TRUE)
#if(!(DF %in% vt$meta$ID)) {
# stop("The tag ", DF, " does not appear to be in the data...")
#}
# extract the matrix as an 012 file
dgt <- vcfR::extract.gt(v, element = "GT")
d012 <- make_it_012(dgt)
dimnames(d012) <- dimnames(dgt)
# now get the read depth matrix
dp <- vcfR::extract.gt(v, element = "DP")
storage.mode(dp) <- "integer"
# now, if some of the markers have been imputed, but the read depths added back on there
# there will be a genotype call, even though the DP field is a ".". Those .'s will
# have been converted to NAs, and we will now turn those into 0s. If the genotype
# is really not called (a -1 below...) then it will get turned back into an NA.
dp[is.na(dp)] <- 0
dp[d012 == -1] <- NA
# OK, now dp is a matrix of read depths with NAs where the genotype was unobserved
# now we need to bin those depths up
bd <- bin_depths(D = dp, S = minBin)
bd$dp_bins <- t(bd$dp_bins)
list(mat012 = t(d012),
dp_bins_list = bd)
}
```

**Any scripts or data that you put into this service are public.**

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.