Create a Predefined Coding Category Filter

Source: R/variant_filter.R

Convenience constructor that returns a glow_variant_filter with the standard STAARpipeline boolean mask for a coding category.

coding_filter(
  category,
  rare_maf_cutoff = 0.01,
  min_mac = 1L,
  min_variants = 2L
)

Arguments

category

Character: one of "plof", "plof_ds", "missense", "disruptive_missense", "synonymous", "ptv", "ptv_ds".

rare_maf_cutoff

Numeric MAF ceiling. Default 0.01.

min_mac

Integer minimum cohort MAC. Default 1 (exclude variants monomorphic in the analysis cohort).

min_variants

Integer minimum variants. Default 2.

Value

A glow_variant_filter S3 object with a category_name attribute.

Examples

# Predefined coding category filters
spec_plof <- coding_filter("plof")
spec_plof
#> GLOWr Variant Filter Specification
#>   Variant type: SNV 
#>   MAF cutoff: 0.01 
#>   Min MAC: 1 
#>   Min variants: 2 
#>   Category: plof 
#>   Annotation clauses: 6 clause(s)
#>   Required fields: GENCODE.EXONIC.Category, GENCODE.Category 

spec_missense <- coding_filter("missense", rare_maf_cutoff = 0.05)

# Available categories:
# "plof", "plof_ds", "missense", "disruptive_missense",
# "synonymous", "ptv", "ptv_ds"