mp_aggregate_clade-methods: calculate the mean/median (relative) abundance of internal...

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

calculate the mean/median (relative) abundance of internal nodes according to their children tips.

Description

calculate the mean/median (relative) abundance of internal nodes according to their children tips.

Usage

mp_aggregate_clade(
  .data,
  .abundance = NULL,
  force = FALSE,
  relative = TRUE,
  aggregate_fun = c("mean", "median", "geometric.mean"),
  action = "get",
  ...
)

## S4 method for signature 'MPSE'
mp_aggregate_clade(
  .data,
  .abundance = NULL,
  force = FALSE,
  relative = TRUE,
  aggregate_fun = c("mean", "median", "geometric.mean"),
  action = "get",
  ...
)

## S4 method for signature 'tbl_mpse'
mp_aggregate_clade(
  .data,
  .abundance = NULL,
  force = FALSE,
  relative = TRUE,
  aggregate_fun = c("mean", "median", "geometric.mean"),
  action = "get",
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_aggregate_clade(
  .data,
  .abundance = NULL,
  force = FALSE,
  relative = TRUE,
  aggregate_fun = c("mean", "median", "geometric.mean"),
  action = "get",
  ...
)

Arguments

.data	MPSE object which must contain otutree slot, required
.abundance	the column names of abundance.
force	logical whether calculate the (relative) abundance forcibly when the abundance is not be rarefied, default is FALSE.
relative	logical whether calculate the relative abundance.
aggregate_fun	function the method to calculate the (relative) abundance of internal nodes according to their children tips, default is 'mean', other options are 'median', 'geometric.mean'.
action	character, "add" joins the new information to the otutree slot if it exists (default). In addition, "only" return a non-redundant tibble with the just new information. "get" return a new 'mpse', which the features is the internal nodes.
...	additional parameters, meaningless now.

Value

a object according to 'action' argument.

Examples

## Not run: 
  suppressPackageStartupMessages(library(curatedMetagenomicData))
  xx <- curatedMetagenomicData('ZellerG_2014.relative_abundance', dryrun=F)
  xx[[1]] %>% as.mpse -> mpse
  otu.tree <- mpse %>% 
    mp_aggregate_clade(
      .abundance = Abundance, 
      force = TRUE, 
      relative = FALSE,
      action = 'get' # other option is 'add' or 'only'.
    )
  otu.tree

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.