Returns the glow_variant_filter that the sets of one gene-centric
non-coding mask are extracted under: the run's filter copied (QC label and
pass value, variant type, MAF cutoff, minimum MAC, minimum set size) with
no annotation clause, because the mask's selection and its gene linkage
are done once per chromosome by define_regions_noncoding,
whose candidates already satisfy the mask. The grouping pass applies the
QC label and the variant type; the per-set extraction applies those again
together with the run's MAF cutoff, minimum MAC and minimum set size.
The filter carries the mask's name as the attribute category_name
(as coding_filter does) and its specification as
mask.
noncoding_filter(category, filter_spec)One of the eight mask names: "upstream",
"downstream", "UTR", "promoter_CAGE",
"promoter_DHS", "enhancer_CAGE", "enhancer_DHS",
"ncRNA". The masks are described in
define_regions_noncoding.
The run's glow_variant_filter, from
variant_filter. Its annotation clauses, if any, are not
copied.
A glow_variant_filter with the attributes
category_name and mask.
run_filter <- variant_filter(rare_maf_cutoff = 0.01, min_variants = 2L)
spec <- noncoding_filter("enhancer_DHS", run_filter)
spec
#> GLOWr Variant Filter Specification
#> Variant type: SNV
#> MAF cutoff: 0.01
#> Min MAC: 1
#> Min variants: 2
#> Category: enhancer_DHS
#> Annotation filter: none (all passing variants)
attr(spec, "category_name")
#> [1] "enhancer_DHS"