filter_batch | R Documentation |
This function applies anpan::read_and_filter() to a set of files.
filter_batch(
bug_dir,
meta_file,
filter_stats_dir,
pivot_wide = TRUE,
minmax_thresh = NULL,
covariates = NULL,
outcome = NULL,
filtering_method = "kmeans",
discretize_inputs = TRUE,
discard_poorly_covered_samples = TRUE,
omit_na = FALSE,
plot_ext = "pdf",
verbose = TRUE
)
bug_dir |
a directory of gene family files |
meta_file |
path to a metadata tsv |
filter_stats_dir |
directory to save filtering statistics to |
pivot_wide |
logical indicating whether to return data in wide format |
minmax_thresh |
genes must have at least this many (or N - this many)
non-zero observations or else be discarded. NULL defaults to |
covariates |
covariates to account for (as a vector of strings) |
outcome |
the name of the outcome variable |
filtering_method |
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 |
discard_poorly_covered_samples |
logical indicating whether to discard samples where the genes of a bug are poorly covered |
omit_na |
logical indicating whether to omit incomplete cases of the metadata |
plot_ext |
extension to use for plots |
A list of filtered data frames
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