mp_rrarefy-methods: mp_rrarefy method

In xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

mp_rrarefy method

Description

mp_rrarefy method

Usage

mp_rrarefy(
  .data,
  .abundance = NULL,
  raresize,
  trimOTU = FALSE,
  trimSample = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'MPSE'
mp_rrarefy(
  .data,
  .abundance = NULL,
  raresize,
  trimOTU = FALSE,
  trimSample = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_rrarefy(
  .data,
  .abundance = NULL,
  raresize,
  trimOTU = FALSE,
  trimSample = FALSE,
  seed = 123,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_rrarefy(
  .data,
  .abundance = NULL,
  raresize,
  trimOTU = FALSE,
  trimSample = FALSE,
  seed = 123,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of OTU(feature) abundance column, default is Abundance.
raresize	integer Subsample size for rarefying community.
trimOTU	logical Whether to remove the otus that are no longer present in any sample after rarefaction
trimSample	logical whether to remove the samples that do not have enough abundance (raresize), default is FALSE.
seed	a random seed to make the rrarefy reproducible, default is 123.
...	additional parameters, meaningless now.

Value

update object

Author(s)

Shuangbin Xu

See Also

[mp_extract_assays()] and [mp_decostand()]

Examples

data(mouse.time.mpse)
mouse.time.mpse %>% mp_rrarefy()

xiangpin/MicrobiotaProcess documentation built on April 14, 2024, 10:10 a.m.