README.md

In jcrodriguez1989/mGSZ2:

mGSZ2

Improved Modified Gene Set Z-score method for gene set analysis.

mGSZ2 is an improved version of the functional analysis mGSZ R library.

Improvements

• Runs multicore by implementing the BiocParallel library.
• Allows the use of any desired genes ranking function.
• Has internally implemented the best-evaluated gene ranking method to perform functional analysis of RNA-Seq data.
• As output it returns the gene set score. Positive or negative depending on enriching condition.
• As output it returns the genes list that contributed to enrich each gene set, i.e., genes conforming the enrichment score leading edge.
• Provides a Shiny-based graphical interface by the startMGSZZ2() function.
• Displays the results of the gene sets by enrichment plots.

Installation

In R console type:

R > install.packages('devtools');
R > library(devtools);
R > install_github('jcrodriguez1989/mGSZ2');

Usage

R > library('mGSZ2');
R >
R > # to start the GUI:
R > # startMGSZ2();
R >
R > # Load example data
R > data(dummyData); # list that contains 'x', 'y', 'l'.
R > # x is the expression matrix (genes as rows, samples as cols), y are the gene sets
R > # l are the conditions (one for each sample from x).
R >
R > set.seed(8818);
R > mGSZres <- mGSZ2(dummyData$x, dummyData$y, dummyData$l);
R > head(mGSZres);
gene.sets     pvalue mGszScore                                        impGenes
set9       set9 0.05117402  1.952384 g55, g70, g68, g30, g51, g81, g44, g88, g75, g5
set8       set8 0.06463807 -2.146767     g50, g92, g71, g54, g10, g46, g87, g13, g48
set16     set16 0.10781461  1.907799 g53, g22, g68, g2, g18, g32, g80, g15, g63, g25
set2       set2 0.12166137  2.124259                              g1, g61, g100, g67
set1       set1 0.13451610 -1.879446                                    g4, g50, g11
set7       set7 0.15552483  1.503978                                         g1, g76
R >
R > # enrichment plot of the set9 gene set
R > enrichmentPlot(mGSZres, 'set9');

jcrodriguez1989/mGSZ2 documentation built on May 24, 2019, 9:51 a.m.