Get housekeeping genes from global expression profile

Get housekeeping genes from global expression profile

Usage

get_HK(exp)

Arguments

exp

A gene expression data frame with genes in row names and samples in column names or a `SummarizedExperiment` object.

Value

Character vector of housekeeping gene IDs.

Details

This function identifies housekeeping genes, which are broadly expressed genes with low variation in a global scale across samples. For some cases, users would want to remove these genes as they are not interesting for coexpression network analyses. See references for more details.

References

Machado, F.B., Moharana, K.C., Almeida‐Silva, F., Gazara, R.K., Pedrosa‐Silva, F., Coelho, F.S., Grativol, C. and Venancio, T.M. (2020), Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas. Plant J, 103: 1894-1909.

Author

Fabricio Almeida-Silva

Examples

data(zma.se)
hk <- get_HK(zma.se)