anpan: Run anpan

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Run anpan

Description

Run the anpan gene model on a single bug

Usage

anpan(
  bug_file,
  meta_file,
  out_dir,
  genomes_file = 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,
  skip_large = TRUE,
  save_fit = TRUE,
  discard_poorly_covered_samples = TRUE,
  plot_ext = "pdf",
  save_filter_stats = TRUE,
  verbose = TRUE,
  ...
)

Arguments

bug_file	path to a gene family file (usually from HUMAnN)
meta_file	path to a metadata tsv
out_dir	path to the desired output directory
genomes_file	optional file giving gene presence/absence of representative isolate genomes
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	covariates to account for (as a vector of strings)
outcome	the name 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)).
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".
discard_poorly_covered_samples	logical indicating whether to discard samples where the genes of a bug are poorly covered
plot_ext	extension to use for plots
save_filter_stats	logical indicating whether to save filter statistics
...	arguments to pass to [cmdstanr::sample()] if applicable

Details

The specified metadata file must contain columns matching "sample_id" and the specified covariates and outcome variables.

If provided, genomes_file is used to refine the filtering process. The format must be genes as rows, with the first column giving the gene id (usually a UniRef90 identifier), and subsequent columns representing isolate genomes. The entries of the isolate genome columns should give 0/1 indicators of whether or not the gene is present in the isolate. The gene counts present in these isolates are used to establish the typical number of genes present in a strain of the species and a lower threshold on the number of acceptable gene observations. If >=5 isolate genomes are available, the lower threshold is 2 standard deviations below the mean, otherwise it is 2/3 of the mean.

Value

a data.table of model statistics for each gene

See Also

[anpan_batch()]

biobakery/anpan documentation built on July 26, 2024, 11:19 p.m.