ps_drop_incomplete: Deselect phyloseq samples with sample_data missings

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Deselect phyloseq samples with sample_data missings

Description

Check phyloseq object sample_data for missing values (NAs)

• specify which variables to check with vars argument, or check all

• drop samples with any missings

Usage

ps_drop_incomplete(ps, vars = NA, verbose = FALSE)

Arguments

ps	phyloseq with sample_data
vars	vector of variable names to check for missings (or NA, which uses all variables in sample data)
verbose	message about number of samples dropped if verbose not FALSE, (and only if > 0 samples dropped) and message about number of missing per variable in vars if verbose = "max" (and message even if 0 samples dropped)

Details

This is a wrapper for stats::complete.cases function.

Value

phyloseq

See Also

ps_filter

Examples

library(phyloseq)
data("enterotype", package = "phyloseq")

enterotype
ps_drop_incomplete(enterotype)
ps_drop_incomplete(enterotype, vars = "Enterotype", verbose = TRUE)
ps_drop_incomplete(enterotype, vars = "Sample_ID", verbose = TRUE)
ps_drop_incomplete(enterotype, vars = c("Enterotype", "Sample_ID"))
ps_drop_incomplete(enterotype, verbose = "max")

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.