phyloseq_summary: Summary for phyloseq objects.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Summary for phyloseq objects.

Description

This function could be used for comparison of multiple phyloseq objects (e.g., after trimming).

Usage

phyloseq_summary(physeq, ..., cols = NULL, more_stats = FALSE, long = FALSE)

Arguments

physeq	A phyloseq-class object
...	Optionally more phyloseq objects
cols	Character vector with column names for phy1 & phy2 in the resulting table
more_stats	Logical; if TRUE, some additional OTU abundance statistics will be calculated
long	Logical; if TRUE, results will be returned in a long format

Details

Optionally (if more_stats = TRUE), some additional OTU abundance statistics may be estimated (min, max, median, Q1, Q3, and CQV of OTU abundance). Coefficient of quartile variation (a.k.a., Quartile coefficient of dispersion) is preferred to the 'classical' coefficient of variation for the analysis of samples from nonnormal distributions. It is estimated by the following formula: (Q3-Q1)/(Q3+Q1), where Q1 is the population 25th percentile and Q3 is the population 75th percentile.

Value

Data frame with number and percentage of OTUs.

Examples

# Load data
data(esophagus)

# Single sample summary
phyloseq_summary(esophagus, cols = "Esophagus")
phyloseq_summary(esophagus, cols = "Esophagus", more_stats = T)

## Compare trimmed and raw data
# Remove taxa that have less than 5 reads
eso_trim <- prune_taxa(taxa_sums(esophagus) >= 5, esophagus)

phyloseq_summary(esophagus, eso_trim, cols = c("Esophagus", "Trimmed_esophagus"))
phyloseq_summary(esophagus, eso_trim, cols = c("Esophagus", "Trimmed_esophagus"), more_stats = T)

eso_trim2 <- phyloseq_filter_top_taxa(esophagus, perc = 20)
phyloseq_summary(esophagus, eso_trim, eso_trim2, cols = c("Esophagus", "Trimmed_1", "Trimmed_2"), more_stats = T)

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.