tests/testthat/_snaps/accessors.md

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

biom_info

Code
  biom_info(hmp50)
Output
  $id
  [1] "Human Microbiome Project - 50 Sample Demo"

  $type
  [1] "OTU table"

  $format
  [1] "1.0.0"

  $format_url
  [1] "http://biom-format.org"

  $generated_by
  [1] "rbiom 1.0.2.9026"

  $date
  [1] "2021-07-01T18:48:45Z"

  $matrix_type
  [1] "sparse"

  $matrix_element_type
  [1] "int"

  $shape
  [1] 490  50

  $comment
  [1] ""

sample_sums

Code
  sample_sums(hmp5)
Output
  HMP01 HMP02 HMP03 HMP04 HMP05 
   1660  1371  1353  1895  3939

Code
  sample_sums(hmp5, long = TRUE)
Output
    Sample Reads
  1  HMP01  1660
  2  HMP02  1371
  3  HMP03  1353
  4  HMP04  1895
  5  HMP05  3939

Code
  sample_sums(hmp5, long = TRUE, md = TRUE)
Output
    Sample Reads Age BMI     Body Site    Sex
  1  HMP01  1660  22  20 Buccal mucosa Female
  2  HMP02  1371  24  23 Buccal mucosa   Male
  3  HMP03  1353  28  26        Saliva   Male
  4  HMP04  1895  25  23        Saliva   Male
  5  HMP05  3939  27  24 Buccal mucosa Female

Code
  sample_sums(min5, long = TRUE, md = TRUE)
Output
    Sample Reads
  1  HMP01  1660
  2  HMP02  1371
  3  HMP03  1353
  4  HMP04  1895
  5  HMP05  3939

rarefaction_level

Code
  rarefaction_level(hmp5)
Output
  NULL

Code
  rarefaction_level(rare5)
Output
  [1] 1353

Code
  rarefaction_level(as_percent(rare5))
Output
  [1] 1

has_tree

Code
  has_tree(hmp5)
Output
  [1] TRUE

Code
  has_tree(min5)
Output
  [1] FALSE

has_sequences

Code
  has_sequences(hmp5)
Output
  [1] TRUE

Code
  has_sequences(min5)
Output
  [1] FALSE

is_rarefied

Code
  is_rarefied(hmp5)
Output
  [1] FALSE

Code
  is_rarefied(rare5)
Output
  [1] TRUE

n_samples

Code
  n_samples(hmp5)
Output
  [1] 5

n_otus

Code
  n_otus(hmp5)
Output
  [1] 132

n_ranks

Code
  n_ranks(hmp5)
Output
  [1] 6

Code
  n_ranks(min5)
Output
  NULL

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.