Skip to contents

Filter data based on DArT reproducibility statistics

Source: R/filter_dart_reproducibility.R
filter_dart_reproducibility.Rd

This filter removes markers below a certain threshold. Based on the repoducibility column found in DArT files.

Filter target: Markers.

Statistics: Reproducibility (established by DArT)

Usage

filter_dart_reproducibility(
  data,
  interactive.filter = TRUE,
  filter.reproducibility = 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.reproducibility

(double, character) This is best decided after viewing the figures. Usually values higher than 0.95 are not uncommon. The value can also be character: filter.reproducibility = "outliers". Using this, will remove outlier markers using the lower outlier statistics. Default: filter.reproducibility = 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. Diagnostic files, marker lists, and filtering parameters are written to the output folder.

Interactive version

The function first displays and writes the DArT reproducibility distribution and helper outputs. It then asks the following questions:

  1. "Do you still want to blacklist markers? (y/n):"

  2. If yes, choose 1 to use the lower boxplot-outlier statistic or 2 to enter a threshold.

  3. With option 2, answer "Enter the proportion threshold (0-1), the minimum reproducibility tolerated:".

Markers with reproducibility below the selected threshold are blacklisted. Answering no leaves the data unchanged. Use interactive.filter = FALSE with an explicit filter.reproducibility for a reproducible analysis.

Examples

if (FALSE) { # \dontrun{
spotted.cod <- genometranslator::read_dart(
    data = "Combined_1514and1614_SNP_80Callrate.csv",
    strata = "strata.dart.spotted.cod.tsv"
)
turtle.filtered <- radr::filter_dart_reproducibility(
    data = spotted.cod,
    interactive.filter = FALSE,
    filter.reproducibility = 0.97
)
} # }