GenStatR: Generation of differential expression statistics
In FEM: Identification of Functional Epigenetic Modules

Description Usage Arguments Value Author(s) References

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.

1	GenStatR(exp.m,pheno.v)

`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.

`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.

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

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

FEM documentation built on April 28, 2020, 8:56 p.m.