metaAnalysisDE {DExMA}R Documentation

Performing Meta-analysis

Description

It performs meta-analysis using eight different methods.

Usage

metaAnalysisDE(
    objectMA,
    typeMethod = c("FEM", "REM", "maxP", "minP", "Fisher", 
                    "Stouffer"),
    missAllow = 0.3,
    proportionData = 0.5
)

Arguments

objectMA

A list of list. Each list contains two elements. The first element is the expression matrix (genes in rows and sample in columns) and the second element is a vector of zeros and ones that represents the state of the diffenrent samples of the expression matrix. 0 represents one group (controls) and 1 represents the other group (cases). The result of the CreateobjectMA can be used too.

typeMethod

A character that indicates the method to be peformed. See "Details"for more information

missAllow

a number that indicates the maximun proportion of missing values allowed in a sample. If the sample has more proportion of missing values the sample will be eliminated. In the other case the missing values will be imputed using the K-NN algorithm.

proportionData

The minimum proportion of datasets in which a gene must be contained to be included. By default, the gene must be contained in at least half of the datasets

Details

The different meta-analysis method that can be applied are:

  1. Effects sizes methods:

  2. P-value combination mehods

Value

A dataframe with the meta-analysis results. Depending on the applied method, a different dataframe is obtained. For more information see the package vignette.

Author(s)

Juan Antonio Villatoro Garcia, juanantoniovillatorogarcia@gmail.com

References

Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Jordi Martorell-Marugán, Yolanda Román-Montoya, Marta E Alarcón-Riquelme, Pedro Carmona-Sáez, A survey of gene expression meta-analysis: methods and applications, Briefings in Bioinformatics, 2020;, bbaa019, https://doi.org/10.1093/bib/bbaa019

Michael Dewey (2020). metap: meta-analysis of significance values.

Examples

data(DExMAExampleData)
ResultsMA <- metaAnalysisDE(objectMA=maObject, typeMethod="REM",
                            missAllow=0.3, proportionData=0.5)
ResultsMA

[Package DExMA version 1.0.2 Index]