subset_marker: Subset microbiome markers

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Subset microbiome markers

Description

Subset markers based on an expression related to the columns and values within the marker_table slot of mm.

Usage

subset_marker(mm, ...)

Arguments

mm	a microbiomeMarker or marker_table object.
...	the subsetting expression passed to base::subset().

Value

a subset object in the same class with mm.

Examples

data(enterotypes_arumugam)
mm <- run_limma_voom(
    enterotypes_arumugam,
    "Enterotype",
    contrast = c("Enterotype 3", "Enterotype 2"),
    pvalue_cutoff = 0.01,
    p_adjust = "none"
)
subset_marker(mm, pvalue < 0.005)

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.