difftest {microbial} | R Documentation |
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 |
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")