differential_abundance: Differential abundance analysis

In compbiomed/animalcules: Interactive microbiome analysis toolkit

Differential abundance analysis

Description

Differential abundance analysis

Usage

differential_abundance(
  MAE,
  tax_level,
  input_da_condition = c(),
  input_da_condition_covariate = NULL,
  min_num_filter = 5,
  input_da_padj_cutoff = 0.05,
  method = "DESeq2"
)

Arguments

MAE	A multi-assay experiment object
tax_level	The taxon level used for organisms
input_da_condition	Which condition is the target condition
input_da_condition_covariate	Covariates added to linear function
min_num_filter	Minimum number reads mapped to this microbe
input_da_padj_cutoff	adjusted pValue cutoff
method	choose between DESeq2 and limma

Value

A output dataframe

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
differential_abundance(toy_data,
  tax_level = "phylum",
  input_da_condition = c("DISEASE"),
  min_num_filter = 2,
  input_da_padj_cutoff = 0.5,
  method = "DESeq2"
)

compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.