ohtadstats (version 2.1.1)

dwrapper: Ohta D Statistic Wrapper

Description

Pairwise computation of Ohta's D Statistics for each pair of polymorphisms in a given dataset.

Usage

dwrapper(data_set, tot_maf = 0.1, pop_maf = 0.05)

Arguments

data_set

Matrix containing genotype data with individuals as rows and loci as columns. Genotypes should be coded as 0 (homozygous), 1 (heterozygous), or 2 (homozygous). Rownames must be subpopulation names and column names should be marker names.

tot_maf

Minimum minor allele frequency across the total population for a marker to be included in the analysis.

pop_maf

Minimum minor allele frequency across a subpopulation for that subpopulation to be included in analysis.

Value

A list of matrices containing the pairwise comparisons for each D statistic. Also included is the number of subpopulations evaluated in each comparison and the ratio of d2is_mat to d2st_mat (ratio1) and dp2st_mat to dp2is_mat (ratio2). The result of a comparison between marker M and marker N will be found in the Mth row at the Nth column.

Details

This wrapper implements the dstat function for all pairs of loci in a genotype matrix. If the input matrix includes n loci, choose(n,2) pairs are evaluated. Therefore, the computaiton time scales quadratically, and is not feasible for large datasets. We suggest manual parallelization across computational nodes for a large-scale (ie thousands of markers) implementation.

Examples

# NOT RUN {
data(beissinger_data)
beissinger_subset <- beissinger_data[,1:15]
dwrapper(beissinger_subset, tot_maf = 0.05, pop_maf = 0.01)

# }
# NOT RUN {
data(beissinger_data)
dwrapper(beissinger_data, tot_maf = 0.05, pop_maf = 0.01)
# }