normalize: Normalize metannotate data

In MetAnnotate/metannoviz: Process and visualize output from the MetAnnotate pipeline

Description

Double-normlizes metannotate data by HMM length and a single-copy gene marker. The input data has to be pre-mapped and collapsed by taxonomy

Usage

normalize(metannotate_data, normalizing_HMM = "rpoB")

Arguments

metannotate_data	Tibble of taxonomy-collapsed and mapped metannotate data - see collapse_by_taxon
normalizing_HMM	Character vector (length 1) giving the plotting name of an HMM.Family in your table that you want to normalize all genes within each sample to. This should be a reliable single-copy taxonomic marker gene, e.g., rpoB, dnaK, and so on.

Value

List of two:

• Tibble of metannotate data; 'hits' has now been changed to 'percent_abundance' and is double-normalized

• Tibble summarizing total normalized counts for genes

MetAnnotate/metannoviz documentation built on Aug. 2, 2020, 3:12 p.m.