DA_wrapper: Wrapper function for differential abundance calling

In kimberlyroche/codaDE: What the Package Does in One 'Title Case' Line

Wrapper function for differential abundance calling

Description

Wrapper function for differential abundance calling

Usage

DA_wrapper(
  ref_data,
  data,
  groups,
  method = "NBGLM",
  oracle_calls = NULL,
  control_indices = NULL
)

Arguments

ref_data	absolute abundance data set (samples x features)
data	relative abundance data set (samples x features)
groups	group (cohort) labels
method	differential abundance calling method (e.g. "DESeq2")
oracle_calls	optional baseline (true) differential abundance calls
control_indices	if specified, these features are used as the stable features against which to normalize observed abundances (DESeq2-only)

Value

named list of baseline (true) differential abundance calls and calls made on relative abundances (the observed data)

kimberlyroche/codaDE documentation built on May 11, 2022, 12:40 a.m.