WhamFrom16s: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

In zc1286/Wham: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

Description

R package allowing for exploratory analysis of metagenomics and metatranscriptomic data. Includes visualization and statistical analysis on the gene family and taxa level. This package is developped based on package ALDEx2.

Usage

WhamFrom16s(
  taxaCount = NULL,
  colData = NULL,
  design = NULL,
  phyloseq_object = NULL
)

Arguments

taxaCount	a data frame or a matrix contains the counts generated from the 16s process. The first column of the count table have to be "Taxa"(case insensitive)
colData	metadata table contains experiment design with at least one column. The row number of coldata has to be equal to the columns of count table excluding the first three columns.
design	a formula expresses how the counts for each genes depend on the variables.e.g ~ group
phyloseq_object	object from package phyloseq

Value

a WhamInput object contains countData, ColData, design, Taxainfo, FeatureInfo, TaxaTable

Examples

# see the vignette for more details

zc1286/Wham documentation built on May 14, 2021, 8 p.m.