tidyDGEL: Create a DGEL object from tidy table

In bulksoil/tidyMB: A Set of Tools for Tidy Microbiome Analysis

Description

This function will take the long table and return a DGEL object either from edgeR or DESeq2. At the moment, it can only do simple designs (limited to one factor).

Usage

tidyDGEL(x, method = "edgeR", samples = "SampleID", otus = "variable",
  value = "value", group_column = NULL, formula = NULL)

Arguments

method	The method for doing differential gene expression. Defaults to edgeR.
samples	The column header for your sample identifiers. Defaults to SampleID.
otus	The column header for your OTU identifiers. Defaults to variable.
value	The column header for the OTU abundances. Defaults to RA.
group	The variable that the user is trying to differentiate. Needs to be a column in the dataset.

Value

tibble of OTUs by Sample IDs

Examples

widen()

bulksoil/tidyMB documentation built on May 29, 2019, 2:27 p.m.