Reset filters (individuals and markers) in radiator GDS object.

List current active filters in radiator GDS object. Reset specific filters or all filters at once.

reset_filters(
  gds,
  list.filters = TRUE,
  reset.all = FALSE,
  filter.individuals.missing = FALSE,
  filter.individuals.heterozygosity = FALSE,
  filter.individuals.coverage.total = FALSE,
  detect.mixed.genomes = FALSE,
  detect.duplicate.genomes = FALSE,
  filter.reproducibility = FALSE,
  filter.monomorphic = FALSE,
  filter.common.markers = FALSE,
  filter.ma = FALSE,
  filter.mean.coverage = FALSE,
  filter.genotyping = FALSE,
  filter.snp.position.read = FALSE,
  filter.snp.number = FALSE,
  filter.short.ld = FALSE,
  filter.long.ld = FALSE,
  filter.hwe = FALSE,
  filter.whitelist = FALSE
)

Arguments

gds

(2 options) A Genomic Data Structure (GDS) file or object

How to get GDS ? Look into tidy_genomic_data, read_vcf, tidy_vcf or write_gds.

list.filters

filters (logical, optional) List current active filters for individuals and markers. Default: list.filters = TRUE.

reset.all

(logical, optional) Reset all individuals and markers filters. Default: reset.all = FALSE.

filter.individuals.missing

(logical, optional) Default: filter.individuals.missing = FALSE.

filter.individuals.heterozygosity

(logical, optional) Default: filter.individuals.heterozygosity = FALSE.

filter.individuals.coverage.total

(logical, optional) Default: filter.individuals.coverage.total = FALSE.

detect.mixed.genomes

(logical, optional) Default: detect.mixed.genomes = FALSE.

detect.duplicate.genomes

(logical, optional) Default: detect.duplicate.genomes = FALSE.

filter.reproducibility

(logical, optional) Default: filter.reproducibility = FALSE.

filter.monomorphic

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

filter.common.markers

(logical, optional) Default: filter.common.markers = FALSE.

filter.ma

(logical, optional) Default: filter.ma = FALSE.

filter.mean.coverage

(logical, optional) Default: filter.mean.coverage = FALSE.

filter.genotyping

(logical, optional) Default: filter.genotyping = FALSE.

filter.snp.position.read

(logical, optional) Default: filter.snp.position.read = FALSE.

filter.snp.number

(logical, optional) Default: filter.snp.number = FALSE.

filter.short.ld

(logical, optional) Default: filter.short.ld = FALSE.

filter.long.ld

(logical, optional) Default: filter.long.ld = FALSE.

filter.hwe

(logical, optional) Default: filter.hwe = FALSE.

filter.whitelist

(logical, optional) Default: filter.whitelist = FALSE.

See also

sync_gds, list_filters.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) {
# List active filters for individuals and markers
reset_filters(gds)

# You changed your decision concerning the genotyping threshold or
# entered the wrong one:
reset_filters(gds, filter.genotyping = TRUE)
}