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

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

Description

Workflow Hub for Automated Metagenomic Exploration (WHAM!)

Usage

WhamFromEBI(
  DE = c("feature", "taxa"),
  featureCount = NULL,
  taxaCount = NULL,
  colData = NULL,
  design = NULL
)

Arguments

DE	required. Type of differential expression. Options are "taxa",or "feature".
featureCount	a data frame or a matrix contains the feature counts generated from the EBI process. The first two columns of the count table have to be "Acc" ,and "Feature" respectively(case insensitive)
taxaCount	a data frame or a matrix contains the taxa counts generated from the EBI process. The first column of the count table have to be "taxa" respectively(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

Value

a WhamInput object contains taxaCount/featureCount, ColData, design, Taxainfo, FeatureInfo, TaxaTable

Examples

# see the vignette for more details

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