filter_gf: Filter a gene family file
In biobakery/anpan: Quantifying Microbial Strain-Host Associations

filter_gf

R Documentation

Filter a gene family file

Description

This is the function that anpan uses to filter an input genefamily data.table. This can be useful if you want to play around with different filtering options without repeatedly re-reading or checking the file.

Usage

filter_gf(
  gf,
  samp_stats,
  filtering_method = "kmeans",
  covariates = NULL,
  outcome = NULL,
  genomes_file = NULL,
  discard_poorly_covered_samples = TRUE,
  save_filter_stats = FALSE,
  filter_stats_dir = NULL,
  plot_ext = "pdf",
  bug_name = NULL
)

Arguments

`gf`	a gene family data.table
`samp_stats`	a data.table of sample statistics
`filtering_method`	method to use for filtering samples. Either "kmeans" or "none"
`covariates`	covariates to account for (as a vector of strings)
`outcome`	the name of the outcome variable
`genomes_file`	optional file giving gene presence/absence of representative isolate genomes
`discard_poorly_covered_samples`	logical indicating whether to discard samples where the genes of a bug are poorly covered
`save_filter_stats`	logical indicating whether to save filter statistics
`filter_stats_dir`	directory to save filtering statistics to
`plot_ext`	extension to use for plots