findTaxonMat: Find the Taxonomy Information Matrix

In mani2012/PathoStat: PathoStat Statistical Microbiome Analysis Package

Description

Find the Taxonomy Information Matrix

Usage

findTaxonMat(names, taxonLevels)

Arguments

names	Row names of the taxonomy matrix
taxonLevels	Taxon Levels of all tids

Value

taxmat Taxonomy Information Matrix

Examples

example_data_dir <- system.file("example/data", package = "PathoStat")
pathoreport_file_suffix <- "-sam-report.tsv"
datlist <- readPathoscopeData(example_data_dir, pathoreport_file_suffix,
input.files.name.vec = as.character(1:6))
dat <- datlist$data
ids <- rownames(dat)
tids <- unlist(lapply(ids, FUN = grepTid))
# taxonLevels <- findTaxonomy(tids[1:5])
# taxmat <- findTaxonMat(ids[1:5], taxonLevels)

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