get_rep_seqs_from_otus: Returns representative 16S sequences for a set of...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Returns representative 16S sequences for a set of closed-reference OTU IDs

Description

Returns representative 16S sequences for a set of closed-reference OTU IDs

Usage

get_rep_seqs_from_otus(
  otus,
  database = database_choices[2],
  rep_seq_path = "data/rep_seqs/"
)

Arguments

otus	List of OTU IDs
database	Database/method used for generating populations in the table - currently Greengenes or SILVA
rep_seq_path	File path to OTU representative sequences

Value

Biostrings object containing representative sequences for each OTU in order

Examples

get_rep_seqs_from_otus(otu_list, "Greengenes 13_5 or 13_8", "data/rep_seqs/")

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.