obtain_block_abundances: Obtain block abundances

In surh/wheelP: Designing synthetic bacterial communities for predictable plant phenotypes

Description

Takes a Dataset object, pools samples and taxa according to specified variables, and returns adata frame that contains the average abundance by taxa group per group of samples

Usage

obtain_block_abundances(Dat, varnames = c("Bacteria", "Replicate",
  "Experiment", "Pre.Pi", "Pos.Pi"), taxa.group = "Block", sep = "_",
  taxa2rm = "contaminant")

Arguments

Dat	a dataset object
varnames	Vector of character strings that name the variables to be used to pool samples. Must correspond to variables in the Map attribute of Dat.
taxa.group	Character string indicating the variable for collapsing taxa.
sep	Separator character for creating composite variables.
taxa2rm	Taxa IDs to remove.

Value

A data frame that contains the average abundance by taxa group per group of samples.

Author(s)

Sur Herrera Paredes

surh/wheelP documentation built on May 7, 2019, 10:11 a.m.