mock2: Bias experiment data

In PERFect: Permutation filtration for microbiome data

Description

These publicly available data (Brooks et al., 2015) were generated as a part of a study designed to evaluate the bias at each step of the VCU sequencing protocol, namely, DNA extraction, PCR amplification, sequencing and taxonomic classification. Mock community samples were created out of 7 vaginally relevant bacteria by mixing prescribed quantities of cells, with quantities varying across samples according to an experimental design described in Brooks et al, 2015. As opposed to the positive controls data, bacteria appear in different proportions across samples. The number of taxa identified by the sequencing and bioinformatics pipeline was 46.

Usage

data(mock2)

Format

This file contains a count OTU table and a proportion OTU table, each with 240 samples and 46 taxa. A list of true taxa is also given.

PERFect documentation built on Nov. 8, 2020, 7:43 p.m.