testRelations: testRelations
In eprifti/momr: Mining Metaomics Data (MetaOMineR)

testRelations

R Documentation

testRelations

Description

This function applies a statistical test either a correlation (spearman, pearson), wilcoxon or t.test as a function of a given phenotype. It will return a matrix of probabilities p and q values along with the correlation coefficient or the enrichment variable when a binary parameter.

Usage

testRelations(
  data,
  trait,
  type,
  restrict = rep(TRUE, ncol(data)),
  multiple.adjust = "BH",
  paired = FALSE,
  debug = FALSE
)

Arguments

`data`	: frequency matrix with gene_ids in the rownames
`trait`	: a vector with the trait to test, binary or numerical variable
`type`	: a character string indicating the type of test to be applied
`restrict`	: an optional logical vector to select a subset of the samples to perform the test default restrict = rep(TRUE, ncol(data)) i.e. all the samples are selected
`multiple.adjust`	: type of multiple adjustment default is "BH" i.e. Benjamini & Hochberg method
`paired`	: logical with default FALSE wether the test should be paired or not
`debug`	: default FALSE, when TRUE the progress is printed each 1000 steps

Details

testRelations

Value

a matrix with analytical results (correlation tests) indicating rho, rho2, p and q values for each parameter tested along with the status of the test

Note

New add on taking into account a trait for correlation, when it is a two class variable with the same number of elements a correlation between both groups is performed