makeGeneTable: makeGeneTable

In SCCC-BBC/PathwaySplice: An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

Description

This function obtains genewise p-values, by representing each gene with the smallest p-value among its features, and then determines genes status as significant or not.

Usage

makeGeneTable(feature.table, sig.threshold = 0.05, stat = "pvalue")

Arguments

feature.table	An featureBasedData object.
sig.threshold	Significance threshold used to determine whether the gene is significant or not
stat	The statistic used to select significant genes. Options are 'pvalue' or 'fdr'

Value

Returns a genewised table with several variables (columns)

geneID	Gene identifiers in ensembl gene IDs
geneWisePvalue	each gene is represented by the smallest p-value among its features
numFeature	number of gene features within the gene
fdr	false discovery rate for genewisePvalue
sig.gene	a gene is significant (1) or not (0)

Examples

data(featureBasedData)
gene.based.table <- makeGeneTable(featureBasedData)

SCCC-BBC/PathwaySplice documentation built on May 9, 2019, 11:07 a.m.