microbiomeMarker {microbiomeMarker} | R Documentation |
This the constructor to build the microbiomeMarker
object, don't
use the new()
constructor.
microbiomeMarker( marker_table = NULL, norm_method = NULL, diff_method = NULL, ... )
marker_table |
a |
norm_method |
character, method used to normalize the input |
diff_method |
character, method used for microbiome marker identification. |
... |
arguments passed to |
a microbiomeMarker
object.
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") )) )