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

Importing Data from BIOM into MicrobiomeStat

Guide to importing BIOM data into MicrobiomeStat data object.

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Last updated 1 year ago

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Follow the instructions below to convert your BIOM data into a format suitable for MicrobiomeStat.

# Example code

# Specify the path to your BIOM data. Replace the placeholder with the correct path on your system.
rich_dense_biom <- "rich_dense_otu_table.biom"
# Reminder: Ensure that you replace the above path with the actual location of your BIOM file.

# Specify the path to your phylogenetic tree. Again, replace the placeholder with the correct path on your system.
treefilename <- "biom-tree.phy"
# Reminder: Ensure that you replace the above path with the actual location of your phylogenetic tree file.

# Convert the BIOM data and associated phylogenetic tree (if provided) 
# into a format suitable for MicrobiomeStat using the mStat_import_biom_as_data_obj function.
data.obj <- mStat_import_biom_as_data_obj(BIOMfilename = rich_dense_biom, treefilename = treefilename)

# The resulting 'data.obj' is now a MicrobiomeStat data object that you can use for further analyses.

By employing the mStat_import_biom_as_data_obj function, the BIOM data, along with optional phylogenetic tree data, can be integrated into the MicrobiomeStat framework. Here's a brief overview of the function's parameters:

  • BIOMfilename: The file path to your BIOM data.

  • treefilename (Optional): The file path to your phylogenetic tree.

  • parseFunction (Optional): A user-defined function to interpret the taxonomy from the BIOM file metadata.

3KB
rich_dense_otu_table.biom
BIOM file containing biological observation matrix and associated metadata.
143B
biom-tree.phy
Phylogenetic tree file representing evolutionary relationships among observed species.
Structure of the MicrobiomeStat data object created from BIOM data.