microbial (version 0.0.21)

difftest: 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
)

Value

datafame with differential test with DESeq2

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

Author

Kai Guo

Examples

 # \donttest{
data("Physeq")
res <- difftest(physeq,group="group")
# }