Find private alleles

Source: R/private_alleles.R

The function highlight private alleles by strata, using a GDS or tidy file or object.

private_alleles(data, strata = NULL, verbose = TRUE)

Arguments

data

(4 options) A file or object generated by radiator:

  • tidy data

  • Genomic Data Structure (GDS)

How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.

strata

(path or object) The strata file or object. Additional documentation is available in read_strata. Use that function to whitelist/blacklist populations/individuals. Option to set pop.levels/pop.labels is also available.

verbose

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Value

A list with an object highlighting private alleles by markers and strata and a second object with private alleles summarized by strata.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) {
corals.private.alleles.by.pop <- radiator::private_alleles(data = tidy, strata = strata.pop)
}