ProcessResults: Retrieve significant pairs, based on adjusted p-values. For...

View source: R/04_ProcessResults.R

ProcessResultsR Documentation

Retrieve significant pairs, based on adjusted p-values. For each pair that is statistically significant, calculate the correlation within group1 (e.g. cancer) and the correlation within group2 (e.g. non-cancer). Users can then remove pairs with a difference in correlations between groups 1 and 2 less than a user-defined threshold.

Description

Retrieve significant pairs, based on adjusted p-values. For each pair that is statistically significant, calculate the correlation within group1 (e.g. cancer) and the correlation within group2 (e.g. non-cancer). Users can then remove pairs with a difference in correlations between groups 1 and 2 less than a user-defined threshold.

Usage

ProcessResults(
  inputResults,
  inputData,
  pvalcutoff = 0.05,
  interactionCoeffPercentile = 0,
  rsquaredCutoff = 0
)

Arguments

inputResults

IntLimResults object with model results (output of RunIntLim())

inputData

MultiDataSet object (output of ReadData()) with analyte levels and associated meta-data

pvalcutoff

cutoff of FDR-adjusted p-value for filtering (default 0.05)

interactionCoeffPercentile

percentile cutoff for interaction coefficient (default bottom 10 percent (high negative coefficients) and top 10 percent (high positive coefficients))

rsquaredCutoff

cutoff for lowest r-squared value

Value

IntResults object with model results (now includes correlations)


IntLIM documentation built on Aug. 22, 2022, 5:05 p.m.