Importing Data from BIOM into MicrobiomeStat

Guide to importing BIOM data into MicrobiomeStat data object.

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

rich_dense_otu_table.biom

3KB

Open

BIOM file containing biological observation matrix and associated metadata.

biom-tree.phy

143B

Open

Phylogenetic tree file representing evolutionary relationships among observed species.

# 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.

Structure of the MicrobiomeStat data object created from BIOM data.

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.