indicator_analysis: Indicator Analysis

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Indicator Analysis

Description

Performs the indicator analysis based on taxonomic summary object

Usage

indicator_analysis(taxobj, taxlevel, func = "r.g", reads = FALSE)

Arguments

taxobj	Configured tax summary objects.See in object_config.
taxlevel	taxonomy levels used for visualization.Must be one of c("Domain","Phylum","Class","Order","Family","Genus","Species","Base").
func	Default: "r.g".The function to use for the indicator analysis, see in multipatt
reads	A logical value indicating whether the input data is in terms of raw reads (TRUE) or relative abundance (FALSE)

Value

A data frame with the results of the indicator analysis, including adjusted p-values, tags and taxonomic information.

Note

This function depends on the following packages: indicspecies, permute. These packages are not automatically loaded and should be installed before using this function.

See Also

multipatt, how

Examples

data("Two_group")
if (requireNamespace("indicspecies", quietly = TRUE) &&
    requireNamespace("permute", quietly = TRUE)) {
  set.seed(999)
  indicator_results <- indicator_analysis(
    taxobj = Two_group,
    taxlevel = "Genus"
  )
  head(indicator_results)
}

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.