makeGeneTable: makeGeneTable

Description Usage Arguments Value Examples

View source: R/Run_pathwaysplice.R

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

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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

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PathwaySplice documentation built on April 28, 2020, 7:44 p.m.