sigPway: A function checks if an object is from the one sample or two...

Description Usage Arguments Details Value Author(s) Examples

View source: R/pipeline.final.R

Description

A function checks if an object is from the one sample or two samples cases and then finds the significant pathways.

Usage

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sigPway(pvalue_results, pvalue)

Arguments

pvalue_results

geneDistributionSet2 object and the output of the pathVarTwoSamples function or geneDistributionSet object and the output of the pathVarOneSample.

pvalue

the significance level to test.

Details

This function takes the output pathVarTwoSamples or pathVarOneSample and returns a significantPathway2 or significantPathway object specifying the significant pathway(s) and which gene(s) belongs to the significant pathway(s).

Value

A significantPathway2 object or significantPathway object is returned.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

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results_2samples=pathVarTwoSamplesCont(bock,pways.kegg,groups=as.factor(c(rep(1,10),rep(2,10))),boot=1000,varStat="sd")
sig_kegg=sigPway(results_2samples,0.05)

jmarlab/pathVar documentation built on May 23, 2019, 9:02 p.m.