Compare Phyloseq Objects

comparePhyloseq(x)

Arguments

x: A named list of phyloseq objects to compare

Value

A tibble

Details

Provided a named list of different phyloseq objects `comparePhyloseq` returns a data.frame with basic values in each of the phyloseq objects.

References

Shetty SA (2021). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
ps1 <- subset_samples(FuentesIliGutData, ILI == "C")
ps1 <- prune_taxa(taxa_sums(ps1) > 0, ps1)

ps2 <- subset_samples(FuentesIliGutData, ILI == "L1")
ps2 <- prune_taxa(taxa_sums(ps2) > 0, ps2)

ps3 <- subset_samples(FuentesIliGutData, ILI == "L2")
ps3 <- prune_taxa(taxa_sums(ps3) > 0, ps3)

ps.list <- c("C" = ps1, "L1" = ps2, "L2" = ps3)

comparePhyloseq(ps.list)
#>   input ntaxa nsample min.reads max.reads total.read average.reads singletons
#> 1     C   901     184     10975    143946    7658743      41623.60          0
#> 2    L1   902     213     12715    140779    8568244      40226.50          0
#> 3    L2   896     192     24868    194135   15127300      78788.02          0
#>    sparsity
#> 1 0.6717355
#> 2 0.6678794
#> 3 0.6372652