runSupertest: Performs statistical tests of the pathway intersections among...
In cavei/MOSClip: Multi Omics Survival Clip

Description Usage Arguments Details Value References

This function calculates intersection sizes among the pathway sets significative in each omic and performs statistical intersection test.

runSupertest(multiPathwayReportData, pvalueThr = 0.05,
  zscoreThr = 0.05, resampligThr = NULL, plot = c("circular",
  "landscape", "noplot"), sort.by = c("set", "size", "degree",
  "p-value"), excludeColumns = NULL, color.on = "#f6bb42",
  color.off = "#D3D3D3")

`multiPathwayReportData`	data.frame, the output of the `multiPathwayReport` or `multiPathwayModuleReport` functions.
`pvalueThr`	numeric indicating the cut-off for overall pvalue
`zscoreThr`	numeric indicating the cut-off for covariates coefficients
`resampligThr`	numeric the number of success in the resamplig procedure
`plot`	character indicating the layout for plotting. It is one of `circular`, `landscape` or `no`. By default, plot="circular", if plot="no" no plot will be provided.
`sort.by`	character indicating how to sort the intersections in the plot. It is one of "set" (by omics), "size" (by intersection size), "degree" (by number of intersected omics), and "p-value".
`excludeColumns`	a vector of characters listing the columns of `multiPathwayReportData` object to be excluded by the analysis. In the case `multiPathwayReportData` derives from `multiPathwayModuleReport` you should set `excludeColumns = c("pathway","module")`.
`color.on`	color that represent the active omics in the sector
`color.off`	color that represent the omics mnot considered in the sector

This function calculates intersection sizes between multiple set of pathways or modules and performs statistical test of the intersections using the total amout of analyzed pathways or modules as background. The super exact test of this function was described in Wang et al 2015.

a data.frame containing all the numeric information of the plot included the pathways shared by different omics.

Minghui Wang, Yongzhong Zhao, and Bin Zhang (2015). Efficient Test and Visualization of Multi-Set Intersections. Scientific Reports 5: 16923.

cavei/MOSClip documentation built on May 12, 2019, 5:22 p.m.