anpan_batch: Apply anpan to a many bugs

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Apply anpan to a many bugs

Description

This function calls anpan() on each gene family file in the bug_dir directory and makes a composite data + results plot for each.

Usage

anpan_batch(
  bug_dir,
  meta_file,
  out_dir,
  genomes_dir = NULL,
  prefiltered_dir = NULL,
  model_type = "fastglm",
  covariates = c("age", "gender"),
  outcome = "crc",
  omit_na = FALSE,
  filtering_method = "kmeans",
  discretize_inputs = TRUE,
  minmax_thresh = NULL,
  discard_poorly_covered_samples = TRUE,
  skip_large = TRUE,
  save_fit = TRUE,
  annotation_file = NULL,
  save_filter_stats = TRUE,
  verbose = TRUE,
  plot_result = TRUE,
  plot_ext = "pdf",
  q_threshold = 0.1,
  beta_threshold = 1,
  n_top = 50,
  width = 10,
  height = 8,
  ...
)

Arguments

bug_dir	a directory of gene family files
meta_file	path to a metadata tsv
out_dir	path to the desired output directory
genomes_dir	an optional directory of genome files
prefiltered_dir	an optional directory to pre-filtered data from an earlier run to skip the filtering step
model_type	either "horseshoe" or "fastglm"
covariates	character vector of covariates to include in the model
outcome	character string of the outcome variable
omit_na	logical indicating whether to omit incomplete cases of the metadata
filtering_method	method to use for filtering samples. Either "kmeans" or "none"
discretize_inputs	logical indicating whether to discretize the input abundance measurements (0/nonzero –> FALSE/TRUE) before passing them to the modelling function
minmax_thresh	genes must have at least this many (or N - this many) non-zero observations or else be discarded. NULL defaults to floor(0.005*nrow(metadata)).
discard_poorly_covered_samples	logical indicating whether to discard samples where the genes of a bug are poorly covered
skip_large	logical indicating whether to skip bugs with over 5k genes. Only used when model_type = "horseshoe".
save_fit	logical indicating whether to save horseshoe fit objects. Only used when model_type = "horseshoe".
annotation_file	a path to a file giving annotations for each gene
save_filter_stats	logical indicating whether to save filter statistics
plot_result	logical indicating whether or not to plot the results
plot_ext	extension to use for plots
q_threshold	FDR threshold to use for inclusion in the plot.
beta_threshold	Regression coefficient threshold to use for inclusion in the plot. Set to 0 to include everything.
n_top	number of top elements to show from the results
width	width of saved plot in inches
height	height of saved plot in inches
...	arguments to pass to [cmdstanr::sample()] if applicable

Details

bug_dir should be a directory of gene (or SNV or pathway) abundance files, one for each bug.

annotation file must have two columns named "gene" and "annotation"

See ?anpan() for the format / usage if providing genome files. If provided, genomes_dir must contain ONLY the genome files themselves.

Value

a data.table of model statistics for each bug:gene combination

See Also

[anpan()]

biobakery/anpan documentation built on Aug. 14, 2024, 8:19 a.m.