remove_duplicates: Read tidy genomic data file ending .rad

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

Read tidy genomic data file ending .rad

Description

Used internally in radiator To remove duplicate individuals based on threshold established from the visualization figures.

Usage

remove_duplicates(
  data = "individuals.pairwise.dist.tsv",
  stats = "genotyped.statistics.tsv",
  dup.threshold = 0.25,
  diff.pop.remove = TRUE,
  path.folder = NULL
)

Arguments

data	(path) The individual's pairwise data. Default: data = "individuals.pairwise.dist.tsv".
stats	(path) The genotype statistics Default: stats = "genotyped.statistics.tsv".
dup.threshold	(double) The threshold to filter out duplicates Default: dup.threshold = 0.25.
diff.pop.remove	Remove all individuals in pairs from different pop. Both samples are potentially problems. With defautl, the function will not keep one sample in the duplicate pair. Default: diff.pop.remove = TRUE.

Value

A list with blacklisted duplicates. Write the blacklist in the working directory.

Author(s)

Thierry Gosselin [e-mail]

thierrygosselin/radiator documentation built on May 5, 2024, 5:12 a.m.