simulate_counts: A function for simulating counts of transcripts.

In TheJacksonLaboratory/HBA-DEALS: Hierarchical Bayesian Analysis of Differential Expression and ALternative SPlicing (HBA-DEALS)

A function for simulating counts of transcripts.

Description

This function prints a table of genes, their corresponding transcripts and simulated counts in multiple sample and two different experimental conditions. It also outputs tables of the differentially expressed genes and the transcripts whose proportions differ between the two conditions.

Usage

simulate(ngenes=10000,invChisq=TRUE,fc=2,equal=TRUE,n1=4,n2=4,base.lib.size=11e6,rseed=2013,num.dif=200,min.nonzero=min(n1,n2),min.counts=10)

Arguments

ngenes	The number of genes to simulate.
invChisq	Whether to use the inverse chi^2 distribution for dispersion. The alternative is log normal.
fc	Fold change of differentially expressed genes.
equal	Whether to simulate equal library sizes. The alternative is fold 10 difference in library size.
n1	Number of sample in the first experimental condition.
n2	Number of sample in the second experimental condition.
base.lib.size	Base library size to simulate.
rseed	Seed for the simulation. The same data will be generated in multiple calls with the same rseed.
num.dif	Num of differentially expressed genes and genes that have differential transcript proportions.
min.nonzero	Minimal number of non-zero entries in each condition that are necessary to keep a row in the generated table.
min.counts	Minimal number counts are necessary to keep a row in the generated table.

Value

The function prints a counts table 'counts.txt', differential genes table 'de_genes.txt' and differential transcripts table 'ds_isoforms.txt' to the working directory.

Author(s)

Guy Karlebach and Peter N Robinson

Examples

 simulate(rseed=1,fc=3,equal=FALSE)

TheJacksonLaboratory/HBA-DEALS documentation built on June 28, 2023, 10:32 a.m.