PathoStat-class: PathoStat class to store PathoStat input data including...

In mani2012/PathoStat: PathoStat Statistical Microbiome Analysis Package

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)

mani2012/PathoStat documentation built on April 3, 2020, 7:41 p.m.