plot_coverage_imbalance_diagnostic: Visual diagnostic of coverage imbalance

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

Visual diagnostic of coverage imbalance

Description

GBS data and STACKS pipeline sometimes output REF and ALT alleles that have coverage imbalance, i.e. the coverage is not equal and skewed towards the REF or ALT alleles. Thw density distribution figure of coverage imbalance between REF and ALT alleles will highlight the problem in you data.

Usage

plot_coverage_imbalance_diagnostic(
  tidy.vcf.file,
  pop.levels,
  read.depth.threshold,
  aes.colour,
  adjust.bin
)

Arguments

tidy.vcf.file	The tidy VCF file created with tidy_genomic_data.
pop.levels	Character string defining your ordered populations.
read.depth.threshold	Define the threshold you wish to analyse.
aes.colour	GGPLOT2 aesthetics, e.g. aes(y = ..count..).
adjust.bin	Adjust GGPLOT2 bin size (0 to 1).

Details

The figures shows the results of the of coverage threshold selected and mean genotype likelihood. You can test different threshold to inspect your data. Ideally the lower left pannel of the 4-plot should be empty. If it is, this shows that setting the threshold of the genotype likelihood filter to the mean or close to it take care of the allelic coverage imbalance. #' e.g. fig <- plot_coverage_imbalance_diagnostic( tidy.vcf.file, pop.levels, read.depth.threshold, aes.colour, adjust.bin) Use ( fig + facet_grid(GROUP_GL ~ GROUP_COVERAGE)). The ratio is calculated : (read depth ALT allele - read depth REF allele)/(read depth ALT allele + read depth REF allele).

Value

4-plots highlighting the different combination of under or over the coverage threshold and mean genotype likelihood. Y- axis show the distribution of genotypes. X- axis show the coverage imbalance the Negative ratio (left x axis) : REF > ALT. Positive ratio (right x axis) : ALT > REF.

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