Rarefy OTU counts.

Sub-sample OTU observations such that all samples have an equal number.

Usage

rarefy(
  biom,
  depth = 0.1,
  n = NULL,
  seed = 0L,
  upsample = NULL,
  clone = TRUE,
  cpus = NULL
)

Arguments

biom

An rbiom object, or any value accepted by as_rbiom().

depth

How many observations to keep per sample. When 0 < depth < 1, it is taken as the minimum percentage of the dataset's observations to keep. Ignored when n is specified. Default: 0.1

n

The number of samples to keep. When 0 < n < 1, it is taken as the percentage of samples to keep. If negative, that number or percentage of samples is dropped. If 0, all samples are kept. If NULL, depth is used instead. Default: NULL

seed

An integer seed for randomizing which observations to keep or drop. If you need to create different random rarefactions of the same data, set the seed to a different number each time.

upsample

If the count data is in percentages, provide an integer value here to scale each sample's observations to integers that sum to this value. Generally not recommended, but can be used to 'shoehorn' metagenomic abundance estimates into rbiom's functions that were designed for amplicon datasets. When invoked, depth, n, and seed are ignored. The default, NULL, will throw an error if the counts are not all integers.

clone

Create a copy of biom before modifying. If FALSE, biom is modified in place as a side-effect. See speed ups for use cases. Default: TRUE

cpus

The number of CPUs to use. Set to NULL to use all available, or to 1 to disable parallel processing. Default: NULL

Value

An rbiom object.

See also

Other transformations: matrix_ops, modify_metadata, slice_metadata, subset(), with()

Examples

    library(rbiom)
    
    sample_sums(hmp50) %>% head()
#> HMP01 HMP02 HMP03 HMP04 HMP05 HMP06 
#>  1660  1371  1353  1895  3939  4150 
    
    biom <- rarefy(hmp50)
    sample_sums(biom) %>% head()
#> HMP01 HMP02 HMP03 HMP04 HMP05 HMP06 
#>  1183  1183  1183  1183  1183  1183