slice_metadata: Subset to a specific number of samples.

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

Subset to a specific number of samples.

Description

Subset to a specific number of samples.

Usage

## S3 method for class 'rbiom'
slice(.data, ..., .by = NULL, .preserve = FALSE, clone = TRUE)

## S3 method for class 'rbiom'
slice_head(.data, n, prop, by = NULL, clone = TRUE, ...)

## S3 method for class 'rbiom'
slice_tail(.data, n, prop, by = NULL, clone = TRUE, ...)

## S3 method for class 'rbiom'
slice_min(
  .data,
  order_by,
  n,
  prop,
  by = NULL,
  with_ties = TRUE,
  na_rm = FALSE,
  clone = TRUE,
  ...
)

## S3 method for class 'rbiom'
slice_max(
  .data,
  order_by,
  n,
  prop,
  by = NULL,
  with_ties = TRUE,
  na_rm = FALSE,
  clone = TRUE,
  ...
)

## S3 method for class 'rbiom'
slice_sample(
  .data,
  n,
  prop,
  by = NULL,
  weight_by = NULL,
  replace = FALSE,
  clone = TRUE,
  ...
)

Arguments

.data	An rbiom object, such as from as_rbiom().
...	For slice(), integer row indexes. For other ⁠slice_*()⁠ functions, not used. See dplyr::slice().
.by, by	<tidy-select> Optionally, a selection of columns to group by for just this operation, functioning as an alternative to group_by(). For details and examples, see ?dplyr_by.
.preserve	Relevant when the .data input is grouped. If .preserve = FALSE (the default), the grouping structure is recalculated based on the resulting data, otherwise the grouping is kept as is.
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
n, prop	Provide either n, the number of rows, or prop, the proportion of rows to select. If neither are supplied, n = 1 will be used. If n is greater than the number of rows in the group (or prop > 1), the result will be silently truncated to the group size. prop will be rounded towards zero to generate an integer number of rows. A negative value of n or prop will be subtracted from the group size. For example, n = -2 with a group of 5 rows will select 5 - 2 = 3 rows; prop = -0.25 with 8 rows will select 8 * (1 - 0.25) = 6 rows.
order_by	<data-masking> Variable or function of variables to order by. To order by multiple variables, wrap them in a data frame or tibble.
with_ties	Should ties be kept together? The default, TRUE, may return more rows than you request. Use FALSE to ignore ties, and return the first n rows.
na_rm	Should missing values in order_by be removed from the result? If FALSE, NA values are sorted to the end (like in arrange()), so they will only be included if there are insufficient non-missing values to reach n/prop.
weight_by	<data-masking> Sampling weights. This must evaluate to a vector of non-negative numbers the same length as the input. Weights are automatically standardised to sum to 1.
replace	Should sampling be performed with (TRUE) or without (FALSE, the default) replacement.

Value

An rbiom object.

See Also

Other transformations: modify_metadata, rarefy(), rarefy_cols(), subset(), with()

Examples

    library(rbiom)
    
    # The last 3 samples in the metadata table.
    biom <- slice_tail(hmp50, n = 3)
    biom$metadata
    
    # The 3 oldest subjects sampled.
    biom <- slice_max(hmp50, Age, n = 3)
    biom$metadata
    
    # Pick 3 samples at random.
    biom <- slice_sample(hmp50, n = 3)
    biom$metadata

rbiom documentation built on April 3, 2025, 6:39 p.m.