biom2generic: Converts biom-object

In larssnip/midiv: MiDiv-lab bioinformatics

Converts biom-object

Description

The content of a biom-object is converted into a readcount-table and a fasta-object and written to files.

Usage

biom2generic(biom.file)

Arguments

biom.file	Name of a biom-file output from DEBLUR,
out.folder	Name of folder to output the resulting files.

Details

This function is used in our DEBLUR pipeline, to convert the output from the biom-file to more generic files containing a readcount- table and sequences in fasta format.

Value

The function will produce two files: The file named readcount_table.txt containing the tab-separated tale of readcounts, one row for each OTU and and column for each sample. The first column is the names of the OTU's. The second file is named centroids.fasta and contains the OTU-sequences, i.e. it has the same number of entries as there are rows in the readcount_table.txt.

Author(s)

Lars Snipen.

larssnip/midiv documentation built on Jan. 20, 2025, 6:22 p.m.