Subset samples using a conditional boolean vector. — subset_samples

The main objective of this function is to complete the phyloseq::subset_samples() function by propose a more easy (but more prone to error) way of subset_samples. It replace the subsetting expression which used the name of the variable in the sam_data by a boolean vector.

Warnings: you must verify the result of this function as the boolean condition must match the order of samples in the sam_data slot.

This function is robust when you use the sam_data slot of the phyloseq object used in physeq (see examples)

Usage

subset_samples_pq(physeq, condition)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
condition: A boolean vector to subset samples. Length must fit the number of samples

Value

a new phyloseq object

Examples


cond_samp <- grepl("A1", data_fungi@sam_data[["Sample_names"]])
subset_samples_pq(data_fungi, cond_samp)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 9 samples ]
#> sample_data() Sample Data:       [ 9 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

subset_samples_pq(data_fungi, data_fungi@sam_data[["Height"]] == "Low")
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 45 samples ]
#> sample_data() Sample Data:       [ 45 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]