createObjectMA: Creation of the object to use in meta-analysis

In Juananvg/DExMA: Differential Expression Meta-Analysis

Creation of the object to use in meta-analysis

Description

It allows the creation of an object to perform meta-analysis.

Usage

createObjectMA(
    listEX,
    listPheno = NULL,
    namePheno = c(rep(1, length(listEX))),
    expGroups = c(rep(1, length(listEX))),
    refGroups = c(rep(2, length(listEX)))
)

Arguments

listEX	A list of dataframes or matrix (genes in rows and sample in columns). A list of ExpressionSets can be used too
listPheno	A list of phenodatas (dataframes or matrix). If the object listEX is a list of ExpressionSets this element can be null.
namePheno	A list or vector of the different colunm names or positions from the phenodatas where the experimental and reference groups are identified. Each element of namePheno correspont to its equivalent element in the listPheno (default a vector of 1, all the first columns of each elements of listPheno are selected).
expGroups	A list of vectors or a vector containing the names or the positions with which we identify the elements of the experiment groups (cases) of the namePheno element (default a vector of 1, all the first groups are selected)
refGroups	A list of vectors or a vector containing the names or the positions with which we identify the elements of the reference groups (control) of the namePheno elements (default a vector of 1, all the first groups are selected)

Value

The object needed to perform meta-analysis. This object is list of nested lists. Each list contains two elements:

• The first element is the expression matrix (genes in rows and sample in columns)

• The second element is a vector of zeros and ones that represents the state of the diffenrent samples of the expression matrix. 0 represents reference group (controls) and 1 represents experimental group (cases).

Author(s)

Juan Antonio Villatoro Garcia, [e-mail]

See Also

elementObjectMA

Examples

data(DExMAExampleData)

phenoGroups = c("condition", "condition", "state", "state")
phenoCases = list(Study1 = "Diseased", Study2 = c("Diseased", "ill"),
                    Study3 = "Diseased", Study4 = "ill")
phenoControls = list(Study1 = "Healthy", Study2 = c("Healthy", "control"),
                        Study3 = "Healthy", Study4 = "control")

newObjectMA <- createObjectMA(listEX=listMatrixEX, listPheno = listPhenodatas, 
                                namePheno=phenoGroups, expGroups=phenoCases, 
                                refGroups = phenoControls)
newObjectMA

Juananvg/DExMA documentation built on Dec. 5, 2023, 1:12 p.m.