MicrobiomeStat Tutorial
  • Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat.
  • INTRODUCTION
    • Exploring MicrobiomeStat: A Consideration for Your Research Toolkit
  • Setting Up MicrobiomeStat: Installation and Data Preparation
    • Installation Guide
    • Creating the MicrobiomeStat Data Object
      • Building MicrobiomeStat from Matrix and Data.frame
      • Converting Data from Phyloseq into MicrobiomeStat
      • Importing Data from QIIME2 into MicrobiomeStat
      • Importing Data from BIOM into MicrobiomeStat
      • Converting SummarizedExperiment into MicrobiomeStat
      • Converting DGEList Data into MicrobiomeStat
      • Converting DESeqDataSet into MicrobiomeStat
      • Importing Data from DADA2 into MicrobiomeStat
      • Importing Data from Mothur into MicrobiomeStat
  • Single-Point Analysis
    • Introduction
    • Alpha Diversity Analysis
    • Beta Diversity Analysis
    • Feature-level Analysis
    • One-Click Reports Generation
  • Paired Samples Analysis
    • Introduction
    • Alpha Diversity Analysis
    • Beta Diversity Analysis
    • Feature-level Analysis
    • One-Click Reports Generation
  • Longitudinal Analysis
    • Introduction
    • Alpha Diversity Analysis
    • Beta Diversity Analysis
    • Feature-level Analysis
    • One-Click Reports Generation
  • Data Manipulation and Transformation
    • Data Summary
    • Data Aggregation
    • Data Normalization
    • Data Filtering
    • Data Validation
    • Data Combination
    • Metadata Management
    • Color Palette
  • Frequently Asked Questions (FAQ)
    • General FAQs
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  1. Setting Up MicrobiomeStat: Installation and Data Preparation
  2. Creating the MicrobiomeStat Data Object

Converting DESeqDataSet into MicrobiomeStat

A guide on converting DESeqDataSet data format into the MicrobiomeStat format.

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Last updated 1 year ago

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This guide provides the recipe for converting the DESeqDataSet format to MicrobiomeStat format.

To begin, let's inspect the initial structure of our DESeqDataSet data:

Proceed with the steps below to conduct the conversion:

# Example Code (replace with your real dataset!)
# Load necessary packages
 library(airway)
 library(DESeq2)

# Load dataset
 data("airway")
 dds <- DESeqDataSet(airway, design = ~ cell + dex)

# Convert DESeqDataSet to MicrobiomeStat data object
 data.obj <- mStat_convert_DESeqDataSet_to_data_obj(dds)

Upon conversion, the data structure will be transformed as follows:

The mStat_convert_DESeqDataSet_to_data_obj function facilitates the transition:

  • dds.obj: The DESeqDataSet object slated for conversion.

After the conversion, the MicrobiomeStat data object consists of:

  • feature.tab: A matrix containing count data.

  • meta.dat: A data frame detailing the sample information.

  • feature.ann: A matrix presenting feature annotations.

For data integrity and relevance, the function ensures only features with a sum > 0 from the counts data are retained.

Initial structure of the DESeqDataSet data.
Structure of the MicrobiomeStat data object after importing DESeqDataSet data.