rmd_conversion: Conversion between log2(RMD) and p-value

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

Conversion between log2(RMD) and p-value

Description

This function provides a conversion between the log base 2 robust Mahalanobis distance value and p-value for output from the rmd_runs function

Usage

rmd_conversion(log2rmd = NULL, pval = NULL, df)

Arguments

log2rmd	numeric log base 2 transformed robust Mahalanobis distance value
pval	numeric p-value associated with rmd_runs algorithm
df	integer value specifying the degrees of freedom associated with the test, which should be equal to the number of metrics used in rmd_runs

Details

Only one of log2rmd and pval should be provided. The input not provided will be solved for based on the provided input.

Value

The function returns the corresponding p-value or log base 2 robust Mahalanobis when the other parameter is specified.

Author(s)

Lisa Bramer

Examples

library(pmartRdata)
mymetab <- edata_transform(
  omicsData = metab_object,
  data_scale = "log2"
)
mymetab <- group_designation(
  omicsData = mymetab,
  main_effects = "Phenotype"
)
rmd_results <- rmd_filter(
  omicsData = mymetab,
  metrics = c("MAD", "Skewness", "Correlation")
)
rmd_conversion(log2rmd = rmd_results$Log2.md, df = 3)

rmd_conversion(pval = .0001, df = 3)
rmd_conversion(log2rmd = 4.5, df = 3)

pmartR/pmartRqc documentation built on March 4, 2024, 3:46 p.m.