microbiomeMarker: Build microbiomeMarker-class objects

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Build microbiomeMarker-class objects

Description

This the constructor to build the microbiomeMarker object, don't use the new() constructor.

Usage

microbiomeMarker(
  marker_table = NULL,
  norm_method = NULL,
  diff_method = NULL,
  ...
)

Arguments

marker_table	a marker_table object differtial analysis.
norm_method	character, method used to normalize the input phyloseq object.
diff_method	character, method used for microbiome marker identification.
...	arguments passed to phyloseq::phyloseq()

Value

a microbiomeMarker object.

See Also

phyloseq::phyloseq()

Examples

microbiomeMarker(
    marker_table = marker_table(data.frame(
        feature = c("speciesA", "speciesB"),
        enrich_group = c("groupA", "groupB"),
        ef_logFC = c(-2, 2),
        pvalue = c(0.01, 0.01),
        padj = c(0.01, 0.01),
        row.names = c("marker1", "marker2")
    )),
    norm_method = "TSS",
    diff_method = "DESeq2",
    otu_table = otu_table(matrix(
        c(4, 1, 1, 4),
        nrow = 2, byrow = TRUE,
        dimnames = list(c("speciesA", "speciesB"), c("sample1", "sample2"))
    ),
    taxa_are_rows = TRUE
    ),
    tax_table = tax_table(matrix(
        c("speciesA", "speciesB"),
        nrow = 2,
        dimnames = list(c("speciesA", "speciesB"), "Species")
    )),
    sam_data = sample_data(data.frame(
        group = c("groupA", "groupB"),
        row.names = c("sample1", "sample2")
    ))
)

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