metahdep (version 1.30.0)

metaprep-class: Class metaprep

Description

This is a class representation for the effect size estimates and other summary information for a single gene, from a collection of gene expression studies, usually constructed in preparation for a meta-analysis.

Objects from the Class

Objects can be created using the function metahdep.format and new.

Slots

theta:

Object of class vector representing the gene's effect size estimates (differential expression measures) from the multiple studies.

V:

Object of class matrix representing the sampling variance/covariance matrix of the gene's effect size estimates from the multiple studies.

X:

Object of class matrix representing the covariate (or design) matrix for the gene. Covariate information from the multiple studies is represented here.

M:

Object of class matrix representing the block diagonal hierarchical structure of effect size estimates from the multiple studies.

max.k:

Object of class integer representing the size of the largest block on the diagonal of M, i.e., the size of the largest hierarchical dependence group for the gene.

row.indices:

Object of class matrix with columns named Study and Row. Optionally returned by the function metahdep.format(), to see which gene (Row) in which ES.obj object (Study) produced the data recorded in each metaprep object.

gene:

Object of class character representing the gene name.

Methods

@

replace the slot entries

References

Stevens J.R. and Nicholas G. (2009), metahdep: Meta-analysis of hierarchically dependent gene expression studies, Bioinformatics, 25(19):2619-2620.

See also the metahdep package vignette.

Examples

###
###  See the metahdep package vignette for a full example 
###
data(HGU.prep.list)
HGU.prep.list[[7]]