pmartR (version 2.4.6)

summary.rmdFilt: RMD Filter Summary

Description

Provide summary of a rmdFilt S3 object

Usage

# S3 method for rmdFilt
summary(object, pvalue_threshold = NULL, ...)

Value

a summary of the p-values associated with running RMD-PAV across all samples. If a p-value threshold is provided the samples that would be filtered at this threshold are reported.

Arguments

object

S3 object of class 'rmdFilt' created by rmd_filter.

pvalue_threshold

A threshold for the Robust Mahalanobis Distance (RMD) p-value. All samples with p-values below the threshold will be filtered out. Default value is NULL. Suggested value is 0.0001

...

further arguments passed to or from other methods

Author

Lisa Bramer, Kelly Stratton

See Also

rmd_filter

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)
mymetab <- group_designation(omicsData = metab_object, main_effects = "Phenotype")
mymetab <- edata_transform(omicsData = mymetab, data_scale = "log2")
myfilt <- rmd_filter(omicsData = mymetab)
summary(myfilt, pvalue_threshold = 0.001)
}