get_sample-methods: Returns all abundance values for species 'i'.

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

Description

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

Usage

get_sample(physeq, i)

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

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

Arguments

physeq	(Required). otu_table-class, or phyloseq-class.
i	(Required). A single taxa/species/OTU ID for which you want to know the abundance in each sample.

Value

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

See Also

get_taxa taxa_names sample_names

Examples

data(esophagus)
taxa_names(esophagus)
get_sample(esophagus, "59_5_19")

Example output

 [1] "59_8_22" "59_5_13" "59_8_12" "65_3_22" "65_5_1"  "65_1_10" "65_7_12"
 [8] "59_6_1"  "65_2_17" "65_9_26" "65_5_18" "65_7_5"  "65_8_12" "65_9_1" 
[15] "59_9_26" "9_6_28"  "65_7_4"  "65_4_26" "9_2_24"  "65_1_17" "65_6_7" 
[22] "9_4_3"   "65_7_18" "65_8_7"  "59_4_5"  "59_5_2"  "65_6_2"  "65_4_10"
[29] "9_7_25"  "9_4_5"   "65_1_8"  "65_2_5"  "59_7_6"  "59_9_31" "9_1_7"  
[36] "9_4_13"  "9_6_3"   "65_4_5"  "59_9_18" "65_9_13" "65_3_18" "65_6_10"
[43] "9_7_18"  "65_8_25" "59_3_5"  "65_8_29" "65_4_20" "59_6_11" "59_9_17"
[50] "9_4_6"   "59_4_25" "59_3_21" "59_3_19" "59_4_16" "59_8_3"  "59_5_19"
[57] "65_9_9"  "59_2_6" 
 B  C  D 
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phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.