Applies quality filtering of loci by applying a maximum amount of missing data allowed per locus above which loci are discarded

Source: R/data_readiness.R

miss_threshold takes a "missingness" threshold and applies it to a filtered numerical allele data set and then writes the results to csv.

miss_threshold(mt, at)

Arguments

mt

Numeric value of the "missingness" threshold to further filter the numerical alleles. Values less than the threshold are retained.

at

Numeric value of the average amplification threshold used on the input data. NOTE used to select a pre-made data.

Value

Writes a numerical alleles data csv, filtered to the `at` and `mt` thresholds, to the `results/` sub-directory. It will also print to screen the number of loci that will be filtered out at this "missingness" threshold.

Details

The predetermined "missingness" threshold, ascertained through visualisation miss_hist, is used to further filter the numerical alleles data set and written to csv to the `results/` sub-directory.

The amplification threshold parameter is used to select the correct data set from the `results/` sub-directory that had been created by the amp_threshold function.

Author

Bart Huntley, bart.huntley@dbca.wa.gov.au

For more details see https://dbca-wa.github.io/ScatMatch/index.html the ScatMatch website

Examples

if (FALSE) {
miss_threshold(mt = 0.2, at = 0.8)
}