runSupertest: Performs statistical tests of the pathway intersections among...

Description Usage Arguments Details Value References

Description

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

Usage

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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")

Arguments

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

Details

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.

Value

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

References

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.