pairwiseMatrixTest: Generic pairwise matrix test

In martingarridorc/biokit: Toolkit for the automatic analysis of omics data

Description

Compare two pieces of data from a matrix given a sample information data frame and a grouping column.

Usage

pairwiseMatrixTest(
  mat,
  sampInfo,
  groupCol,
  numerator,
  denominator,
  metricFun = defaultLogFc,
  statFun = nsTestT,
  sigFun = nsTestPValue,
  pAdjustMethod = "BH",
  allowNa = TRUE,
  featName = "feature",
  metricName = "logFc",
  statName = "t",
  pValName = "pValue",
  pAdjName = "pAdj"
)

Arguments

mat	Matrix containing data to be analyzed.
sampInfo	Sample information data frame.
groupCol	Name of the sampInfo column containing the grouping variable.
numerator	Label of the grouping variable to be used as numerator.
denominator	Label of the grouping variable to be used as denominator.
metricFun	Function to calculate metric of change. Defaults to log2(ratio of means).
statFun	Function to calculate statistic of change. Defaults to a non-sensitive T-Test T value.
sigFun	Function to calculate significance of change. Defaults to a non-sensitive T-Test P value.
pAdjustMethod	Method used to adjust P values.
allowNa	Allow NAs on input matrix?
featName	Name of the column containing the compared features (rows).
metricName	Name of the column containing the metric.
statName	Name of the column containing the statistic.
pValName	Name of the column containing the p values.
pAdjName	Name of the column containing the adjusted p values.

Value

A data frame with the row-wise statistical results.

martingarridorc/biokit documentation built on June 28, 2021, 12:24 a.m.