bog_subset: Subset OTU table by sampling site

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Returns an OTU table containing only samples from the identified sampling site. This function can also be used on tables of higher level taxa generated by combine_otus(), or on tables that have already been processed by year_subset().

Usage

bog_subset(bog_id, table)

Arguments

bog_id	The three letter code indicating the sampling site. The bog is represented by letters one and two; options are TB, SS, CB, NS, MA, HK, WS, and FB. The third letter indicates the layer; E for epilimnion and H for hypolimnion. The bog_id should be in quotes, and regular expressions can be used.
table	A table containing the relative abundances of each taxon as rows and samples as columns. Sample names must be coded in the format bog, layer, date, and replicate (example: TBE07JUN08.R2 == Trout Bog Epilimnion, collected 07Jun08, replicate 2)

Value

Returns a relative abundance table containing samples from the specified sampling site in columns, with taxa in rows

Author(s)

Alexandra Linz <[e-mail]>

Examples

data(otu_table)

Trout_Bog_Epilimnion <- bog_subset("TBE", otu_table)

Hells_Kitchen_Hypolimnion <- bog_subset("HKH", otu_table)

# Include both epilimnion and hypolimnion in a single table
Trout_Bog_both_layers <- bog_subset("TB.", otu_table)

# Include all meromictic hypolimnia
meromictic_hypolimnia <- bog_subset("HKH|MAH", otu_table)

OTUtable documentation built on May 1, 2019, 10:51 p.m.