lrTestBias: lrTestBias

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

Description

This function tests presence of selection bias using logistic regression, and produces a boxplot that compares distributions of bias factors (e.g. number of exons) for significant genes and non-significant genes.

Usage

lrTestBias(genewise.table, boxplot.width = 0.1)

Arguments

genewise.table	A dataframe with genewise p-value for each gene, returned from makeGeneTable()
boxplot.width	width of boxplot

Details

To determine presentce of selection bias, we fit the following logistic regression model:

Pr(a gene is significant) ~ number of features within the gene

Here features refer to exon bins or splicing junction bins, depending on how genewise pvalues were obtained in the genewise.table

Value

Nothing to be returned

Examples

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

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