private_alleles: Find private alleles

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Find private alleles

Description

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

Usage

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(s)

Thierry Gosselin [e-mail]

Examples

## Not run: 
corals.private.alleles.by.pop <- radiator::private_alleles(data = tidy, strata = strata.pop)

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.