private_haplotypes: private haplotypes

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

private haplotypes

Description

Minor Allele Frequency filter.

Usage

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

Arguments

data	A tidy genomic dataframe Used internally in radiator and might be of interest for users. How to get a tidy data frame ? Look into radiator tidy_genomic_data.
strata	(optional) A strata file or object in the global environment. The strata is a tab-separated data frame with 2 columns: INDIVIDUALS and STRATA. If used, the strata will replace the current STRATA or POP_ID in the dataset. Use this argument if you want to find private haplotypes on another hierarchical level, other than POP_ID.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Value

A list with private haplotypes per markers and strata and a summary of overall number of private haplotypes per strata.

Author(s)

Thierry Gosselin [e-mail]

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