deseq2_analysis: Differential expression analysis

In ericjcgalvez/MicrobiomeWrangler:

Differential expression analysis

Description

Test for differential expression based on negative binomal distribution

Usage

deseq2_analysis(
  phylo,
  var,
  alpha = 0.01,
  test = "Wald",
  fitType = "parametric"
)

Arguments

phylo	Phyloseq Object with OTU table and sample data
var	Variable of sample data to analyze
test	significance test used in DESeq2. Either "Wald" or "LRT"
fitType	type of fitting of dispersions to the mean intensity in DESeq2. Either "parametric", "local" or "mean"

Value

DESeqDataSet object including data set and test results

Examples

data("mice_B6_N")
desq2_analysis(mice_B6_N, "Vendor")

ericjcgalvez/MicrobiomeWrangler documentation built on April 14, 2022, 6:33 p.m.