difftest: Calculate differential bacteria with DESeq2

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

Calculate differential bacteria with DESeq2

Description

Calculate differential bacteria with DESeq2

Usage

difftest(
  physeq,
  group,
  ref = NULL,
  pvalue = 0.05,
  padj = NULL,
  log2FC = 0,
  gm_mean = TRUE,
  fitType = "local",
  quiet = FALSE
)

Arguments

physeq	A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
group	group (DESeq2). A character string specifying the name of a categorical variable containing grouping information.
ref	reference group
pvalue	pvalue threshold for significant results
padj	adjust p value threshold for significant results
log2FC	log2 Fold Change threshold
gm_mean	TRUE/FALSE calculate geometric means prior to estimate size factors
fitType	either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity.
quiet	whether to print messages at each step

Value

datafame with differential test with DESeq2

Author(s)

Kai Guo

Examples

 
data("Physeq")
res <- difftest(physeq,group="group")

guokai8/microbial documentation built on Oct. 15, 2024, 11:32 p.m.