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Filter markers mean coverage

Source: R/filter_coverage.R
filter_coverage.Rd

This function is designed to remove/blacklist markers based on mean coverage information.

Filter target: Markers.

Statistics: Mean marker coverage. Genotype read depth is averaged across active individuals for each marker.

Usage

filter_coverage(
  data,
  interactive.filter = TRUE,
  filter.coverage = NULL,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE,
  ...
)

Arguments

data

A tidy genomic data frame or another genomic object supported by the calling function.

interactive.filter

Logical indicating whether an interactive filtering session may display diagnostics and ask for thresholds. Default: interactive.filter = TRUE.

filter.coverage

(optional, string) 2 options:

  • character string filter.coverage = "outliers" will use as thresholds the lower and higher outlier values in the box plot.

  • numeric vector filter.coverage = c(10, 200) for the marker mean-coverage lower and upper bounds.

Default: filter.coverage = NULL.

filename

(optional, character) Default: filename = NULL.

parallel.core

Number of workers available for parallel operations. Default: parallel.core = parallel::detectCores() - 1.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = TRUE.

...

Additional arguments passed to lower-level screening or filtering functions.

Value

The filtered data in the same representation as the input. GDS marker metadata and active variants are updated in place, so the underlying GDS file is modified. Coverage tables, figures, marker lists, and filtering parameters are written to the function output folder when applicable.

Advanced mode

dots-dots-dots ... allows to pass several arguments for fine-tuning the function:

  1. filter.common.markers (optional, logical). Default: filter.common.markers = FALSE, Documented in filter_common_markers.

  2. filter.monomorphic (logical, optional) Should the monomorphic markers present in the dataset be filtered out ? Default: filter.monomorphic = TRUE. Documented in filter_monomorphic.

  3. path.folder: to write ouput in a specific path (used internally in radr). Default: path.folder = getwd(). If the supplied directory doesn't exist, it's created.

Interactive version

The interactive mode first calculates marker coverage, writes and displays the coverage distribution and helper plots, and then asks:

  1. "Choose the min mean coverage threshold (e.g. 7 or 10):"

  2. "Choose the max mean coverage threshold (e.g. 100 or 300):"

Markers outside the inclusive interval are blacklisted. Use interactive.filter = FALSE with an explicit two-value filter.coverage for a reproducible analysis.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
genome <- genometranslator::read_genome("my_genome.gds")

# Inspect marker coverage and choose lower and upper limits interactively.
genome <- radr::filter_coverage(data = genome)

# Alternatively, start from a separate unfiltered GDS for a scripted run.
scripted_genome <- genometranslator::read_genome("my_genome_scripted.gds")
scripted_genome <- radr::filter_coverage(
  data = scripted_genome,
  interactive.filter = FALSE,
  filter.coverage = c(10, 200)
)
} # }