SplatPopParams: The SplatPopParams class

In splatter: Simple Simulation of Single-cell RNA Sequencing Data

Description

S4 class that holds parameters for the splatPop simulation.

Parameters

In addition to the SplatParams parameters, splatPop simulation requires the following parameters:

[similarity.scale]

Scaling factor for pop.cv.param.rate, where values larger than 1 increase the similarity between individuals in the population and values less than one make the individuals less similar.

[eqtl.n]

The number (>1) or percent (<=1) of genes to assign eQTL effects.

[eqtl.dist]

Maximum distance between eSNP and eGene

[eqtl.maf.min]

Minimum Minor Allele Frequency of eSNPs.

[eqtl.maf.max]

Maximum Minor Allele Frequency of eSNPs.

[eqtl.group.specific]

Percent of eQTL effects to simulate as group specific.

eQTL Effect size distribution parameters. Defaults estimated from GTEx eQTL mapping results, see vignette for more information.

eqtl.ES.shape

Shape parameter for the effect size gamma distribution.

eqtl.ES.rate

Rate parameter for the effect size gamma distribution.

Bulk Mean Expression distribution parameters. Defaults estimated from GTEx data, see vignette for more information.

pop.mean.shape

Shape parameter for the mean (i.e. bulk) expression gamma distribution

pop.mean.rate

Rate parameter for the mean (i.e. bulk) expression gamma distribution

Bulk Expression Coefficient of Variation distribution parameters binned. Defaults estimated from GTEx data, see vignette for more information.

pop.cv.param

Dataframe containing gene mean bin range, and the CV shape, and CV rate parameters for each of those bins.

The parameters not shown in brackets can be estimated from real data using splatPopEstimate. For details of the eQTL simulation see splatPopSimulate.

splatter documentation built on Dec. 3, 2020, 2:01 a.m.