Run_pathwaysplice: Run_pathwaysplice

In aiminy/PathwaySplice: An R Package for Adjusting Bias in Gene Set Enrichment Analysis

Description

Perform pathwaysplice in one step

Usage

Run_pathwaysplice(re.gene.based, ad = "GL", sub_feature = NULL, threshold,
  genomeID, geneID, gene_model, method)

Arguments

re.gene.based	gene based results
ad	bias factor to be adjusted
sub_feature	feature to be checked
threshold	threshold to be used for adjustment
genomeID	gene to be used
geneID	geneID to be used
gene_model	gene model to be used
method	method to be used

Value

a list that has gene set enrichment analysis results

Examples

data(mds)
data(hg19)

Example.Go.adjusted.by.exon<-Run_pathwaysplice(mds,ad='exon_SJ',sub_feature='E',
0.05,genomeID='hg19',geneID='ensGene',gene_model=hg19,method='Wallenius')

Example.Go.adjusted.by.exon<-Run_pathwaysplice(mds,ad='exon_SJ',sub_feature='E',
0.05,genomeID='hg19',geneID='ensGene',gene_model=hg19,method='Sampling')

Example.Go.unadjusted<-Run_pathwaysplice(mds,ad='exon_SJ',sub_feature='E',
0.05,genomeID='hg19',geneID='ensGene',gene_model=hg19,method='Hypergeometric')

aiminy/PathwaySplice documentation built on May 10, 2019, 7:38 a.m.