get_taxa-methods: Returns all abundance values of sample 'i'.

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

This is a simple accessor function for investigating a single sample-of-interest.

Usage

get_taxa(physeq, i)

## S4 method for signature 'otu_table'
get_taxa(physeq, i)

## S4 method for signature 'phyloseq'
get_taxa(physeq, i)

Arguments

physeq	(Required). otu_table-class, or phyloseq-class.
i	(Required). A single sample for which you want to know the abundance of each species. Can be integer for index value, or sample name.

Value

An integer vector of the abundance values for each species in physeq for sample i

See Also

get_sample taxa_names sample_names

Examples

data(esophagus)
sample_names(esophagus)
get_taxa(esophagus, "B")

Example output

[1] "B" "C" "D"
59_8_22 59_5_13 59_8_12 65_3_22  65_5_1 65_1_10 65_7_12  59_6_1 65_2_17 65_9_26 
     50       0       2       0       0       0       3       0       6       0 
65_5_18  65_7_5 65_8_12  65_9_1 59_9_26  9_6_28  65_7_4 65_4_26  9_2_24 65_1_17 
      0       0       0       0       0       1       1       0       1       0 
 65_6_7   9_4_3 65_7_18  65_8_7  59_4_5  59_5_2  65_6_2 65_4_10  9_7_25   9_4_5 
      0       1       0       2       0       1       2       0       5       2 
 65_1_8  65_2_5  59_7_6 59_9_31   9_1_7  9_4_13   9_6_3  65_4_5 59_9_18 65_9_13 
      0       1      37       8       1       1       2       0       3       0 
65_3_18 65_6_10  9_7_18 65_8_25  59_3_5 65_8_29 65_4_20 59_6_11 59_9_17   9_4_6 
      1       0       1       1       0       0       0       0       1       2 
59_4_25 59_3_21 59_3_19 59_4_16  59_8_3 59_5_19  65_9_9  59_2_6 
      1       0       0       0       0      14       0      52 

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.