Running gene-set anaysis with `piano`

In piano: Platform for integrative analysis of omics data

Quick start

1. Load piano and example data:

library(piano)
data("gsa_input")

1. Take a look at the structure of the input data:

head(gsa_input$gsc,10)
head(gsa_input$pvals, 10)
head(gsa_input$directions, 10)

1. Load gene-set collection and take a look at the resulting object:

geneSets <- loadGSC(gsa_input$gsc)
geneSets

1. Run gene-set analysis:

gsares <- runGSA(gsa_input$pvals,
                 gsa_input$directions,
                 gsc = geneSets,
                 nPerm = 500) # set to 500 for fast run

Note: nPerm was set to 500 to get a short runtime for this vignette, in reality use a higher number, e.g. 10,000 (default).

1. Explore the results in an interactive Shiny app:

exploreGSAres(gsares)

This opens a browser window with an interactive interface where the results can be explored in detail.

Session info

Here is the output of sessionInfo() on the system on which this document was compiled.

sessionInfo()

piano documentation built on Nov. 8, 2020, 6:27 p.m.