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