IntLIM (version 2.0.2)

ProcessResults: 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
)

Value

IntResults object with model results (now includes correlations)

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