data_load: Read 16S amplicon biom file into phyloseq object

In ericjcgalvez/MicrobiomeWrangler:

Read 16S amplicon biom file into phyloseq object

Description

This function allows you to load the data recived from amplicon sequencing from MIKI-lab.

Usage

data_load(otu, map, tree, min_otu = 0.2, min_sample = 999, verbose = FALSE)

Arguments

otu	character string. Otu_table file path. In biom file oldformat from qiime 1.8.
map	character string. Mapping file path. In biom file oldformat from qiime 1.8.
tree	character string. tree file path. In nexus format from qiime 1.8.
min_otu	numeric. Filter OTUs that do not reach this count number
min_sample	numeric. Filter samples that do not reach this count number
verbose	boolean. If TRUE cat()s step progress

Examples

phylo <- MIKIbiomeR::data_load(otu = otu_path, map = map_path,
tree = tree_path)

ericjcgalvez/MicrobiomeWrangler documentation built on April 14, 2022, 6:33 p.m.