Build or access the marker_table — marker

This is the recommended function for both building and accessing microbiome marker table (marker_table).

marker_table(object)

# S4 method for data.frame
marker_table(object)

# S4 method for microbiomeMarker
marker_table(object)

Arguments

object: an object among the set of classes defined by the microbiomeMarker package that contain marker_table

Value

a marker_table object.

Examples

data(enterotypes_arumugam)
mm <- run_limma_voom(
    enterotypes_arumugam,
    "Enterotype",
    contrast = c("Enterotype 3", "Enterotype 2"),
    pvalue_cutoff = 0.05,
    p_adjust = "fdr"
)
marker_table(mm)
#>                                   feature enrich_group  ef_logFC       pvalue
#> marker1    p__Bacteroidetes|g__Prevotella Enterotype.2  5.821020 3.082538e-11
#> marker2 p__Verrucomicrobia|g__Akkermansia Enterotype.3 -8.620727 3.304924e-05
#> marker3                p__Verrucomicrobia Enterotype.3 -8.266833 6.741864e-05
#>                 padj
#> marker1 7.521392e-09
#> marker2 4.032007e-03
#> marker3 5.483383e-03