filter_individuals: Filter individuals based on genotyping/missingness rate,...

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

Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage

Description

Remove individuals with bad QC based on:

• missingness (genotyping rate)

• heterozygosity

• coverage (total, median, iqr)

Filter targets: Individuals

Statistics: Missingness, heterozygosity and coverage

Used internally in radiator and might be of interest for users who wants to blacklist individuals.

Usage

filter_individuals(
  data,
  interactive.filter = TRUE,
  filter.individuals.missing = NULL,
  filter.individuals.heterozygosity = NULL,
  filter.individuals.coverage.total = NULL,
  filter.individuals.coverage.median = NULL,
  filter.individuals.coverage.iqr = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE,
  ...
)

Arguments

data	(2 options) A Genomic Data Structure (GDS) file or object generated by radiator. How to get GDS? Look into: read_vcf or tidy_vcf.
interactive.filter	(optional, logical) Do you want the filtering session to be interactive. Figures of distribution are shown before asking for filtering thresholds. Default: interactive.filter = TRUE.
filter.individuals.missing	(optional, double) A proportion above which the individuals are blacklisted and removed from the dataset. Default: filter.individuals.missing = NULL.
filter.individuals.heterozygosity	(optional, string of doubles) A proportion below and above which the individuals are blacklisted and removed from the dataset. Default: filter.individuals.heterozygosity = NULL.
filter.individuals.coverage.total	(optional, string of doubles) Target the total coverage per samples. A proportion below and above which the individuals are blacklisted and removed from the dataset. Default: filter.individuals.coverage.total = NULL.
filter.individuals.coverage.median	(optional, string of integers) Target the median coverage per samples. Integers, below and above, that blacklist individuals (removed from the dataset) Default: filter.individuals.coverage.median = NULL.
filter.individuals.coverage.iqr	(optional, string of integers) Target the IQR (Interquartile Range) coverage per samples. Integers, below and above, that blacklist individuals (removed from the dataset) Default: filter.individuals.coverage.iqr = NULL.
parallel.core	(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.
...	(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)

Value

A list with the filtered input and blacklist of individuals.

Author(s)

Thierry Gosselin [e-mail]

See Also

filter_rad tidy_genomic_data, read_vcf, tidy_vcf.

Examples

## Not run: 
require(SeqArray)

# blacklisting outliers individuals:
id.qc <- radiator::filter_individuals(
    data = "my.radiator.gds.rad",
    filter.individuals.missing = "outliers",
    filter.individuals.heterozygosity = "outliers",
    filter.individuals.coverage.total = "outliers")

# using values to blacklist individuals:
id.qc <- radiator::filter_individuals(
    data = "my.radiator.gds.rad",
    filter.individuals.missing = 0.5,
    filter.individuals.heterozygosity = c(0.02, 0.03),
    filter.individuals.coverage.total = c(900000, 5000000))


## End(Not run)

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