filter_by_abundance: Filter normalized metannotate data by relative abundance

Description Usage Arguments Value

View source: R/normalize.R

Description

Filters out low relative abundance taxa from normalized metannotate data based on a desired threshold

Usage

1
filter_by_abundance(metannotate_data, top_x, percent_mode = "within_sample")

Arguments

metannotate_data

Tibble of normalized metannotate data - see normalize

top_x

Numeric vector (length 1) giving the subsetting amount you desire. If top_x >=1, the script will return the "top_x most abundant taxa" for each Dataset/HMM.Family If top_x <1, the script will return "all taxa of (top_x * 100%) abundance or greater for each Dataset/HMM.Family - but see below.

percent_mode

If top_x <1, there are two different methods for keeping the most abundant organisms:

  • "within_sample" – the normalized % abundance relative to rpoB is used

  • "within_HMM" – the percent abundance of that taxon within the specific HMM gene hits is used. You won't notice much of a different between these modes unless one of your HMMs has very few hits and you want to show some of the taxa that were hit. This would be a good time to use 'within_HMM'.

Value

List of two:


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