egsea-aux: EGSEA auxiliary functions

In malhamdoosh/EGSEA: Ensemble of Gene Set Enrichment Analyses

EGSEA auxiliary functions

Description

It lists the accepted sorting methods for analysis results

It lists the p-value combining methods

It lists the supported GSEA methods. Since EGSEA base methods are implemented in the Bioconductor project, the most recent version of each individual method is always used.

This function writes out the official EGSEA package logo

Usage

egsea.sort()

egsea.combine()

egsea.base()

egsea.logo(out.dir = "./")

Arguments

out.dir

character, the target directory to which the logo will be written.

Details

These methods include: ora[1], globaltest[2], plage[3], safe[4], zscore[5], gage[6], ssgsea[7], roast[8], fry[8], padog[9], camera[10] and gsva[11]. The ora, gage, camera and gsva methods depend on a competitive null hypothesis while the remaining seven methods are based on a self-contained hypothesis. Conveniently, EGSEA is not limited to these twelve GSE methods and new GSE tests can be easily integrated into the framework.

Note: the execution time of base methods can vary depending on the size of gene set collections, number of samples, number of genes and number of contrasts. When a gene set collection of around 200 gene sets was tested on a dataset of 17,500 genes, 8 samples and 2 contrasts, the execution time of base methods in ascending order was as follows: globaltest; safe; gage; gsva; zscore; plage; fry; camera; ora; ssgsea; padog. When the same dataset was tested on a large gene set collection of 3,700 gene sets, the execution time of base methods in ascending order was as follows: globaltest; camera; fry; zscore; plage; safe; gsva; ora; gage; padog; ssgsea. Apparently, the size of gene set collection plays a key role in the execution time of most of the base methods. The reduction rate of execution time between the large and small gene set collections varied between 18% and 88%. camera, fry, plage, zscore and ora showed the least reduction rate of execution time. As a result, there is no guarantee that a single combination of base methods would run faster than other combinations. It is worth mentioning that our simulation results showed that the increasing number of base methods in the EGSEA analysis is desirable to achieve high performance.

This function generates a PNG file of the EGSEA logo, which can be used to acknowledge EGSEA in presentations/reports. The logo was designed by Roberto Bonelli from The Walter and Eliza Hall Institute of Medical Research.

Value

It returns a character vector of the accepted values for the sort.by argument in egsea

It returns a character vector of available methods for the combineMethod argument in egsea

It returns a character vector of supported GSE methods.

a PNG file.

References

[1] Tavazoie, S. et al. (1999). Systematic determination of genetic network architecture. Nature Genetics, 22(3), 281-5.
[2] Goeman, J. J. et al. (2004). A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20(1), 93-9.
[3] Tomfohr, J. et al. (2005). Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6, 225.
[4] Barry, W. T. et al. (2005). Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics, 21(9), 1943-9.
[5] Lee, E. et al. (2008). Inferring pathway activity toward precise disease classification. PLoS Computational Biology, 4(11), e1000217.
[6] Luo, W. et al. (2009). GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10, 161.
[7] Barbie, D. A. et al. (2009). Systematic RNA interference reveals that oncogenic KRASdriven cancers require TBK1. Nature, 462(7269), 108-12.
[8] Wu, D. et al. (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics, 26(17), 2176-82.
[9] Tarca, A. L. et al. (2009). A novel signaling pathway impact analysis. Bioinformatics, 25(1), 75-82.
[10] Wu, D. and Smyth, G. K. (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research, 40(17), e133.
[11] Hanzelmann, S. et al. (2013). GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics, 14, 7.

Examples

egsea.sort()

egsea.combine()

egsea.base()

malhamdoosh/EGSEA documentation built on Jan. 28, 2024, 1:17 p.m.