Filter monomorphic markers

Source: R/filter_monomorphic.R

Filter monomorphic markers. This filter will remove from the dataset markers with just one genotype phenotype:

  • genotypes are ALL homozygotes REF/REF (pp)

  • genotypes are ALL heterozygotes REF/ALT, ALT/REF (pq or qp)

  • genotypes are ALL homozygotes ALT/ALT (qq)

Filter targets: SNPs

Statistics: the number of genotype phenotypes

Used internally in radiator and might be of interest for users who wants to keep only polymorphic markers in their dataset.

filter_monomorphic(
  data,
  filter.monomorphic = TRUE,
  parallel.core = parallel::detectCores() - 1,
  verbose = FALSE,
  ...
)

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.

filter.monomorphic

(optional, logical) Default: filter.monomorphic = TRUE.

parallel.core

(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

verbose

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

...

(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

Value

A list with the filtered input, whitelist and blacklist of markers..

Details

Important distinction — genotype-level monomorphism

filter_monomorphic evaluates monomorphism based on the actual genotypes stored inside a GDS file. A marker is considered monomorphic when all non-missing individuals display the same genotype phenotype.

Internally, this is assessed using the variant-level alternate allele dosage ($dosage_alt):


length(unique(g[!is.na(g)])) == 1

This captures cases such as:

  • all REF/REF (dosage = 0)

  • all REF/ALT (dosage = 1)

  • all ALT/ALT (dosage = 2)

Even if the allele frequency in the population is neither 0 nor 1 (e.g., all individuals are REF/ALT heterozygotes), the variant is still considered genotype-monomorphic.

This is a genotype-level definition of polymorphism, which is more conservative and more appropriate for downstream population genomics.

Consequently, filter_monomorphic will often identify additional monomorphic markers that were not removed earlier by filter_monomorphic_vcf, which uses allele-level logic.

This discrepancy is by design.

Note

Why results differ between filter_monomorphic_vcf and filter_monomorphic

These functions intentionally implement two different biological definitions:

  • filter_monomorphic_vcf removes sites that are allele-monomorphic, based on INFO/AC and INFO/AN.

  • filter_monomorphic removes sites that are genotype-monomorphic, based on the distribution of genotype phenotypes in the GDS.

A variant can contain both REF and ALT alleles (allele-level polymorphism) but still have only one genotype phenotype across all individuals. Therefore, it is expected and correct that filter_monomorphic may remove additional markers.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
require(SeqArray) # when using gds
mono <- radiator::filter_monomorphic(data = "my.radiator.gds.rad", verbose = TRUE)
} # }