GenStatR


The gene expression data matrix with rownames annotated to entrez gene
IDs. If there are multiple rows with the same gene ID, function will
average these.


exp.m

pheno.v


Given a gene expression data matrix annotated to entrez gene IDs and a
phenotype vector, it will generate statistics of differential expression
using limma, at the gene-level, for all pairwise comparisons of phenotype levels.


 ~kwd1 

 ~kwd2 

The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.

Andrew E Teschendorff

Identification of Functional Epigenetic Modules

GenStatR function

The gene expression data matrix with rownames annotated to entrez gene
IDs. If there are multiple rows with the same gene ID, function will
average these.

Given a gene expression data matrix annotated to entrez gene IDs and a
phenotype vector, it will generate statistics of differential expression
using limma, at the gene-level, for all pairwise comparisons of phenotype levels.

Generation of differential expression statistics

A list of matrices, from the limma output, ranking genes
  according to differential expression between two phenotypes as
  specified in the contrasts matrix, i.e. top[[i]] will contain the
  ranking for the i'th contrast.

GenStatR: Generation of differential expression statistics

Description

Usage

Arguments

Value

Details

References

See Also

Examples