Subset taxa by position

Select taxa by their integer positions.

Usage

slice_taxa_pq(physeq, ..., clean_phyloseq_object = TRUE)

Arguments

physeq

(phyloseq, required) A phyloseq object.

...

Integer row indices. Positive values select taxa, negative values drop taxa.

clean_phyloseq_object

if TRUE (default), the resulting phyloseq object is cleaned using clean_pq() to remove empty taxa/samples.

Value

A phyloseq object with selected taxa.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Select first 10 taxa
slice_taxa_pq(data_fungi, 1:10)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 10 taxa and 155 samples ]
#> sample_data() Sample Data:       [ 155 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 10 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 10 reference sequences ]

# Remove first 5 taxa
slice_taxa_pq(data_fungi, -(1:5))
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1415 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1415 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1415 reference sequences ]