makeGeneTable {PathwaySplice} | R Documentation

## makeGeneTable

### 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)

[Package PathwaySplice version 1.4.0 Index]