indicator_analysis {LorMe} | R Documentation |
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 |
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 |
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
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)
}
[Package LorMe version 1.1.0 Index]