otus_to_db: Returns AGORA species that a list of Greengenes OTUs were...

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

Returns AGORA species that a list of Greengenes OTUs were mapped to

Description

Returns AGORA species that a list of Greengenes OTUs were mapped to

Usage

otus_to_db(
  otus,
  database = "Greengenes",
  target_db = "AGORA",
  data_prefix = "data/OTU_model_mapping_files/",
  gg_file_prefix = "gg_13_8_99",
  silva_file_prefix = "silva_132_99",
  agora_file_suffix = "_toAGORA_97_map.txt",
  refseq_file_suffix = "_toRefSeq_97_map.txt"
)

Arguments

otus	GG or SILVA OTU abundance table
database	Greengenes or SILVA
target_db	AGORA or RefSeq
gg_file_prefix	File path to output of gg->db vsearch mappings
silva_file_prefix	File path to output of silva->db vsearch mappings
agora_file_suffix	File path to output of xx-> agora vsearch mappings
refseq_file_suffix	File path to output of xx->refseq vsearch mappings

Value

List of AGORA species to use for model building

Examples

otus_to_db(otu_list)

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