getTaxonomyMatrix: Get taxonomy matrix

In BIONF/PhyloProfile: PhyloProfile

Get taxonomy matrix

Description

Get the (full or subset) taxonomy matrix from "data/taxonomyMatrix.txt" based on an input taxon list

Usage

getTaxonomyMatrix(taxDB = NULL, subsetTaxaCheck = FALSE, taxonIDs = NULL)

Arguments

taxDB	Path to the taxonomy DB files
subsetTaxaCheck	TRUE/FALSE subset taxonomy matrix based on input taxon IDs. Default = FALSE
taxonIDs	list of input taxon IDs (e.g. ncbi1234). Default = NULL

Value

Data frame contains the (subset of) taxonomy matrix for list of input taxa.

Author(s)

Vinh Tran [e-mail]

Examples

# get full pre-installed taxonomy matrix
getTaxonomyMatrix()
# get taxonomy matrix for a list of taxon IDs
taxonIDs <- c("ncbi9606", "ncbi10116")
getTaxonomyMatrix(NULL, TRUE, taxonIDs)

BIONF/PhyloProfile documentation built on Nov. 2, 2024, 11:44 p.m.