SimulationSJ2DE: Simulate gene sets based on the number of splicing junctions

In aiminy/GOSJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

Description

We sample the mean of the number of splicing junction, and use this mean to simulate an array A including splicing junction numbers with certain amounts. we convert this number into an array AAA between 0 and 1. Use the median of AAA array as the probability for 1, we sample from [0,1] to get a list with certain length. This list is used as a gene set. For example, if this gene set has 30 genes, each gene has its splicing junction number, we will have 30 splicing junction number. After differential gene expression analysis, some genes are differentiallly expressed, and are labeled as 1,otherwise labeled as 0. Here we simulate two scenarios: Scenario1: the probability of being 1 is dependent on the median of AAA Scenario2: the probability of being 1 is not dependent on the median of AAA

Usage

SimulationSJ2DE(min_num_splicing, max_num_splicing, num_gene)

Arguments

min_num_splicing	minium splicing junction number
max_num_splicing	max splicing junction number
num_gene	number of gene

Value

a list with two set of genes

Examples

re.random.DE2SJ<-SimulationSJ2DE(20,200,30)

aiminy/GOSJ documentation built on May 12, 2019, 3:38 a.m.