Description Usage Arguments Value Examples

bin read depths of SNPs into categories having at least S observations

1 | ```
bin_depths(D, S)
``` |

`D` |
a matrix of read depths. Rows are individuals, columns are SNPs. Cells where data are missing in the genotype matrix must be denoted as NA |

`S` |
the min number of observations to have in each bin |

This returns a list with two components. `dp_bins`

is a matrix of the same
shape as D with the bin categories (as 1, 2, ...) and -1 for this cells
corresponding to missing genotypes. `num_cats`

is the number of depth bins.
`tidy_bins`

is a long format description of the bins.
`bin_stats`

is a tibble giving summary information about the read depth bins which
is useful for plotting things, etc.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# get a matrix of read depths and make it an integer matrix
depths <- vcfR::extract.gt(lobster_buz_2000, element = "DP")
storage.mode(depths) <- "integer"
# get a character matrix of genotypes, so we can figure out which
# are missing and mask those from depths
genos <- vcfR::extract.gt(lobster_buz_2000, element = "GT")
# make missing in depths if missing in genos
depths[is.na(genos)] <- NA
# bin the read depths into bins with at least 1000 observations in each bin
bins <- bin_depths(depths, 1000)
``` |

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.