PathoStat-class {PathoStat} | R Documentation

## PathoStat class to store PathoStat input data including phyloseq object

### Description

Contains all currently-supported BatchQC output data classes:

### Details

slots:

average_count

  a single object of class otu_tableOrNULL

besthit_count

  a single object of class otu_tableOrNULL

highconf_count

  a single object of class otu_tableOrNULL

lowconf_count

  a single object of class otu_tableOrNULL

### Examples

    otumat = matrix(sample(1:100, 100, replace = TRUE), nrow = 10, ncol = 10)
    rownames(otumat) <- paste0("OTU", 1:nrow(otumat))
    colnames(otumat) <- paste0("Sample", 1:ncol(otumat))
    taxmat = matrix(sample(letters, 70, replace = TRUE),
    nrow = nrow(otumat), ncol = 7)
    rownames(taxmat) <- rownames(otumat)
    colnames(taxmat) <- c("Domain", "Phylum", "Class",
    "Order", "Family", "Genus", "Species")
    OTU = phyloseq::otu_table(otumat, taxa_are_rows = TRUE)
    TAX = phyloseq::tax_table(taxmat)
    physeq = phyloseq::phyloseq(OTU, TAX)
    pathostat1(physeq)

[Package PathoStat version 1.13.1 Index]