differential_abundance: Differential abundance analysis

Description Usage Arguments Value Examples

View source: R/differential_abundance.R

Description

Differential abundance analysis

Usage

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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

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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")

hiplot/animalcules documentation built on March 1, 2021, 12:04 a.m.