reset_filters: Reset filters (individuals and markers) in radiator GDS...

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

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

Description

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

Usage

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.

Author(s)

Thierry Gosselin [e-mail]

See Also

sync_gds, list_filters.

Examples

## Not run: 
# 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)

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.