create_phylo: Generic function for creating a phyloseq object from QIIME...
In twbattaglia/btools: A suite of R function for all types of microbial diversity analyses
Description
Usage
Arguments
Value
Description
This function loads an OTU table (.biom format) a phylogenetic tree file (.tre) and
a sample mapping file (.txt/.tsv) to create a standard phyloseq object. Input BIOM file
can be in either JSON format or HDF5.
Usage
1
create_phylo(biom_fp, mappingfile_fp, tree_fp)
Arguments
biom_fp
File location of OTU table in .biom format.
mappingfile_fp
File location of the input sample metadata matching the input OTU table.
tree_fp
File location of the input sample metadata matching the input OTU table.
Value
A phyloseq object to be used downstream for many different analyses.
twbattaglia/btools documentation built on May 3, 2019, 1:51 p.m.
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Description Usage Arguments Value
Description
This function loads an OTU table (.biom format) a phylogenetic tree file (.tre) and a sample mapping file (.txt/.tsv) to create a standard phyloseq object. Input BIOM file can be in either JSON format or HDF5.
Usage
1 | create_phylo(biom_fp, mappingfile_fp, tree_fp)
|
Arguments
biom_fp |
File location of OTU table in .biom format. |
mappingfile_fp |
File location of the input sample metadata matching the input OTU table. |
tree_fp |
File location of the input sample metadata matching the input OTU table. |
Value
A phyloseq object to be used downstream for many different analyses.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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