Chi-squared test assessing the Hardy-Weinberg assumption.

HWE_chisquared performs a per-SNP chi-squared test comparing observed genotype frequencies to those expected when assuming Hardy-Weinberg Equilibrium (HWE). A per-SNP corrected inbreeding coefficient is used if Fmedian is lower than the mathematically minimal possible value of -q/(1-q), with q the minor allele frequency (i.e. this minimum is used instead).

HWE_chisquared(data, inbr = 0, results = NULL)

Arguments

data

List or dataframe. A named list of per-SNP data frames (or one such dataframe) for a single chromosome, with names corresponding to the position on the chromosome. The list contains genotype probabilities ("prr", "prv" and "pvv") for each sample ("sample").

inbr

Number. Estimated or assumed degree of inbreeding within the population under study (default = 0).

results

Data frame. Data frame with SNP results in each row, containing at least the chromosomal position of the SNP (results$position). If NULL, one dataframe is expected as the data input argument.

Value

The results input data frame appended with the following columns:

HWEpval

The p-value of the chi-squared test.

HWE_TestStat

The test statistic of the chi-squared test.