WhamInputfromBiobakery: 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

WhamInputfromBiobakery(
  se = NULL,
  design = NULL,
  TaxaInfo = NULL,
  FeatureInfo = NULL,
  TaxaTable = NULL
)

Arguments

se	a object whose class is the RangedSummarizedExperiment generated from package SummarizedExperiment. Columns of variables indicate sample information in ColData.
design	a formula expresses how the counts for each genes depend on the variables.e.g ~ group
TaxaInfo	a vector indicates the taxanomic information. The length of the vector is equal to the row number of count table.
FeatureInfo	a vector indicates the genomic information. The length of the vector is equal to the row number of count table.
TaxaTable	a data frame whose columns are kindom, phylum, class, order, family, genus and species indicate the taxanomic information. The row number of TaxaTable is equal to the row number of count table

Value

a WhamInput object contains all input information

Examples

# see the vignette for more details

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