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. In case the objectMA has been previously imputed, this element is not necessary.

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. In case the objectMA has been previously imputed, this element is not necessary.

Details

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

  1. Effects sizes methods:

    • "FEM": Fixed Effects model

    • "REM": Random Effects model

  2. P-value combination mehods

    • "Fisher": Fisher's methods

    • "Stouffer": Stouffer's method

    • "maxP": maximum p-value method (Wilkinson's method)

    • "minP": minimum p-value method (Tippet's method)

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 1.2.1 Index]