limmaCompleteTest {DAPAR} | R Documentation

## Computes a hierarchical differential analysis

### Description

This function is a limmaCompleteTest

### Usage

    limmaCompleteTest(qData, sTab, comp.type = "OnevsOne")

### Arguments

`qData` | A matrix of quantitative data, without any missing values.
`sTab` | A dataframe of experimental design (pData()).
`comp.type` | A string that corresponds to the type of comparison. Values are: 'OnevsOne' and 'OnevsAll'; default is 'OnevsOne'.

### Value

A list of two dataframes : FC and P_Value. The first one contains the logFC values of all the comparisons (one column for one comparison), the second one contains the pvalue of all the comparisons (one column for one comparison). The names of the columns for those two dataframes are identical and correspond to the description of the comparison.

### Author(s)

Thomas Burger, Quentin Giai-Gianetto, Samuel Wieczorek

### Examples

    require(DAPARdata)
    data(Exp1_R25_pept)
    obj <- Exp1_R25_pept
    keepThat <- mvFilterGetIndices(obj, 'wholeMatrix', ncol(obj))
    obj <- mvFilterFromIndices(obj, keepThat)
    qData <- Biobase::exprs(obj)
    sTab <- Biobase::pData(obj)
    limma <- limmaCompleteTest(qData,sTab)

[Package DAPAR version 1.12.11 Index]