summary.rmdFilt: RMD Filter Summary

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

RMD Filter Summary

Description

Provide summary of a rmdFilt S3 object

Usage

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

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

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.

Author(s)

Lisa Bramer, Kelly Stratton

See Also

rmd_filter

Examples

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)

pmartR/pmartR documentation built on March 4, 2024, 8:32 a.m.