bin_depths: bin read depths of SNPs into categories having at least S...

In whoa: Evaluation of Genotyping Error in Genotype-by-Sequencing Data

Description

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

Usage

bin_depths(D, S)

Arguments

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

Value

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.

Examples

# 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)

whoa documentation built on Aug. 11, 2021, 9:06 a.m.