get_subset_unique: Unique abundance profile.

In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

Unique abundance profile.

Description

reads the output of the read_interpro or mapping_ko functions to pull out the unique IDs based on metadata. This function identifies the IDs that are only present in a particular metadata group (i.e. KOs only present in environment "a" and absent in the rest of the environments). And retrieves a tibble object.

Usage

get_subset_unique(tibble_rbims, data_experiment, experiment_col, 
experiment_col_element, analysis=c("KEGG", "PFAM", "INTERPRO"))

Arguments

tibble_rbims	a tibble object, created with the read_interpro or mapping_ko functions.
data_experiment	a data frame object that contains the metadata (i.e. taxonomy, sampling site).
experiment_col	a metadata column name. This feature is going to be used for sub-setting.
experiment_col_element	a string of the metadata feature of interest. It is found under the experiment_col column.
analysis	a character, indicating from which input do you want to get the unique abundance profile. Valid options are "KEGG", "PFAM" or "INTERPRO".

Details

This function is part of a package used for the analysis of bins metabolism.

Examples

get_subset_unique(ko_bin_mapp, metadata, Sample_site, 
"Water_column", analysis="KEGG")

mirnavazquez/RbiMs documentation built on Sept. 6, 2024, 1:05 p.m.