measurable_taxa: Identify measurable taxa

In surh/AMOR: Abundance Matrix Operations in R

Identify measurable taxa

Description

Identfies taxa above certain abundance and prevalence thresholds, that can be quantitatively analyzed

Usage

measurable_taxa(...)

## Default S3 method:
measurable_taxa(
  Tab,
  min_reads_otu = 25,
  min_samples_otu = 5,
  method = "absolute",
  table = TRUE
)

## S3 method for class 'Dataset'
measurable_taxa(
  Dat,
  min_reads_otu = 25,
  min_samples_otu = 5,
  method = "absolute",
  table = TRUE,
  clean = TRUE
)

Arguments

Tab	Count table matrix. Samples as columns and OTUs as rows.
method	Either "absolute" (min absolute number of reads in min number of sample) or "AbsProp" (absolute number if reads and proportion of samples).
table	logical indicating whether an abundance table should be returned
Dat	A Dataset object.
clean	logical, indicating whether the function clean should be applied to the result.

Details

Implments abundance filters defined in Benson et al.(2010) & Lundberg et al. (2012). It is recommended to threshold any Dataset before any quantitative analysis.

Value

When table = FALSE, it returns a logical index vector that shows which taxa pass the thresholds.

When table = TRUE, it returns a matrix or Dataset object (depending on the method used), where samples that do not pass the thresholds have been removed

Author(s)

Sur from Dangl Lab.

References

1. Benson AK, Kelly S a, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18933–8. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2973891&tool=pmcentrez&rendertype=abstract

2. Lundberg DS, Lebeis SL, Herrera Paredes S, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. Nature Publishing Group; 2012 Aug 1;488(7409):86–90. Available from: http://www.nature.com/doifinder/10.1038/nature11237

surh/AMOR documentation built on Feb. 21, 2023, 6:31 a.m.