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Deselect phyloseq samples with sample_data missings

Source: R/ps_drop_incomplete.R
ps_drop_incomplete.Rd

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)

Value

phyloseq

Details

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

See also

ps_filter

Examples

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

enterotype
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 280 samples ]
#> sample_data() Sample Data:       [ 280 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]
ps_drop_incomplete(enterotype)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 31 samples ]
#> sample_data() Sample Data:       [ 31 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]
ps_drop_incomplete(enterotype, vars = "Enterotype", verbose = TRUE)
#> Dropping samples with missings: 9
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 271 samples ]
#> sample_data() Sample Data:       [ 271 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]
ps_drop_incomplete(enterotype, vars = "Sample_ID", verbose = TRUE)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 280 samples ]
#> sample_data() Sample Data:       [ 280 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]
ps_drop_incomplete(enterotype, vars = c("Enterotype", "Sample_ID"))
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 271 samples ]
#> sample_data() Sample Data:       [ 271 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]
ps_drop_incomplete(enterotype, verbose = "max")
#> Dropping samples with missings: 249
#> Enterotype has NAs: 9
#> SampleID has NAs: 241
#> Project has NAs: 241
#> Nationality has NAs: 241
#> Gender has NAs: 241
#> Age has NAs: 243
#> ClinicalStatus has NAs: 241
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 553 taxa and 31 samples ]
#> sample_data() Sample Data:       [ 31 samples by 9 sample variables ]
#> tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]