calibrate_alleles: Calibrate REF and ALT alleles based on count

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

Calibrate REF and ALT alleles based on count

Description

Calibrate REF and ALT alleles based on counts. The REF allele is designated as the allele with more counts in the dataset. The function will generate a REF and ALT columns.

reference genome: for people using a reference genome, the reference allele terminology is different and is not based on counts...

Used internally in radiator and might be of interest for users.

Usage

calibrate_alleles(
  data,
  biallelic = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = FALSE,
  ...
)

Arguments

data	A genomic data set in the global environment tidy formats. See details for more info.
biallelic	(optional) If biallelic = TRUE/FALSE will be use during multiallelic REF/ALT decision and speed up computations. Default: biallelic = NULL.
parallel.core	(optional) The number of core used for parallel execution. This is no longer used. The code is as fast as it can. Using more cores will reduce the speed. Default: parallel.core = parallel::detectCores() - 1.
verbose	(optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.
...	(optional) To pass further argument for fine-tuning the tidying (details below).

Details

Input data: A minimum of 4 columns are required (the rest are considered metata info):

1. MARKERS

2. POP_ID

3. INDIVIDUALS

4. GT and/or GT_VCF_NUC and/or GT_VCF

How to get a tidy data frame ? radiator tidy_genomic_data

Value

Depending if the input file is biallelic or multiallelic, the function will output additional to REF and ALT column several genotype codings:

• GT: the genotype in 6 digits format with integers.

• GT_VCF: the genotype in VCF format with integers.

• GT_VCF_NUC: the genotype in VCF format with letters corresponding to nucleotide.

• GT_BIN: biallelic coding similar to PLINK, the coding 0, 1, 2, NA correspond to the number of ALT allele in the genotype and NA for missing genotypes.

Author(s)

Thierry Gosselin [e-mail]

thierrygosselin/radiator documentation built on April 25, 2024, 3:20 a.m.