anpan_batch | R Documentation |
This function calls anpan() on each gene family file in the bug_dir
directory
and makes a composite data + results plot for each.
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,
...
)
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 |
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 |
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.
a data.table of model statistics for each bug:gene combination
[anpan()]
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