Subset samples by position

Select samples by their integer positions.

Usage

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

Arguments

physeq

(phyloseq, required) A phyloseq object.

...

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

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 samples.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Select first 5 samples
slice_samples_pq(data_fungi, 1:5)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 268 taxa and 5 samples ]
#> sample_data() Sample Data:       [ 5 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 268 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 268 reference sequences ]

# Remove first 2 samples
slice_samples_pq(data_fungi, -(1:2))
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1415 taxa and 183 samples ]
#> sample_data() Sample Data:       [ 183 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1415 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1415 reference sequences ]