The write_mothur function will write various file types for use with mothur.
Arguments
- data
A `strollur` object
- dir_path
a string containing the name of directory where the files should be written. Default = current working directory.
- compress
boolean, Default = TRUE.
a vector of strings containing the items you wish to write Options are 'sequence_data', 'bin_data', 'metadata', 'resource_reference', 'sequence_tree', 'sample_tree' and 'report'. By default, everything is written to files.
References
Schloss,P.D., Westcott,S.L., Ryabin,T., Hall,J.R., Hartmann,M., Hollister,E.B., Lesniewski,R.A., Oakley,B.B., Parks,D.H., Robinson,C.J., Sahl,J.W., Stres,B., Thallinger,G.G., Van Horn,D.J. and Weber,C.F. (2009), Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75:7537-7541. <doi:10.1128/AEM.01541-09>
Examples
miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
files <- write_mothur(miseq, tempdir(), compress = FALSE)