Assign marker_table to object

This function replace the marker_table slot of object with value.

marker_table(object) <- value

Arguments

object

a microbiomeMarker object to modify.

value

new value to replace the marker_table slot of object. Either a marker_table-class, a data.frame that can be coerced into marker_table-class.

Value

a microbiomeMarker object.

Examples

data(enterotypes_arumugam)
mm <- run_limma_voom(
    enterotypes_arumugam,
    "Enterotype",
    contrast = c("Enterotype 3", "Enterotype 2"),
    pvalue_cutoff = 0.1,
    p_adjust = "fdr"
)
mm_marker <- marker_table(mm)
mm_marker
#>                                   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
marker_table(mm) <- mm_marker[1:2, ]
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
#>                 padj
#> marker1 7.521392e-09
#> marker2 4.032007e-03