GenStatR {FEM} | R Documentation

## Generation of differential expression statistics

### Description

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.

### Usage

    GenStatR(exp.m,pheno.v)

### Arguments

`exp.m` | 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.
`pheno.v` | The phenotype vector.

### Value

`top` | 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.
`cont` | The contrasts matrix, with columns labeling the contrasts.
`avexp` | The averaged expression matrix at the gene-level.

### Author(s)

"Yinming Jiao"<20907099@zju.edu.cn>, "Andrew E Teschendorff"<andrew@picb.ac.cn>

### References

A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Jiao Y, Widschwendter M, Teschendorff AE. Bioinformatics. 2014;30(16):2360-2366

[Package FEM version 3.12.0 Index]