get_subset_pca: Metabolism PCA.

In mirnavazquez/RbiMs: R Tools for Reconstruncting Bin Metabolisms

Metabolism PCA.

Description

Identifies the most important KO pathways or protein domains in the whole database. And print back a profile of the protein domains that have higher contributions.

Usage

get_subset_pca(tibble_rbims, cos2_val=NULL, 
analysis=c("KEGG", "PFAM", "INTERPRO"))

Arguments

tibble_rbims	a tibble object, created with the read_interpro, mapping_ko or get_subset_* functions.
cos2_val	a numeric vector from 0 to 1 indicating the proportion of contribution used as cut off. Default is 0.98. See get_pca.
analysis	a character, indicating from which input do you want to get the 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_pca(ko_bin_mapp, analysis="KEGG")

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