filter_common_markers: Filter common markers between strata

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

Filter common markers between strata

Description

The function will filter the markers by keeping only those in common between all strata (population or any groupings defined in STRATA column).

Filter targets: SNPs

Statistics: strata genotyping rate per SNPs

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

Usage

filter_common_markers(
  data,
  filter.common.markers = TRUE,
  fig = FALSE,
  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.common.markers	(optional, logical) Default: filter.common.markers = TRUE.
fig	(optional, logical) fig = TRUE will produce an UpSet fig to visualize the number of markers between populations. The package is required for this to work... Default: fig = FALSE.
parallel.core	(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.
verbose	(optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.
...	(optional) To pass further arguments for fine-tuning the function and legacy arguments.

Value

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

Author(s)

Thierry Gosselin [e-mail]

Examples

## Not run: 
require(SeqArray) # when using gds
common <- radiator::filter_common_markers(data = "my.radiator.gds.rad", verbose = TRUE)

## End(Not run)

thierrygosselin/radiator documentation built on May 5, 2024, 5:12 a.m.