splatPopQuantNorm: Quantile normalize by sample to fit sc expression...

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

Quantile normalize by sample to fit sc expression distribution.

Description

For each sample, expression values are quantile normalized (qgamma) using the gamma distribution parameterized from splatEstimate(). This ensures the simulated gene means reflect the distribution expected from a sc dataset and not a bulk dataset.

Usage

splatPopQuantNorm(params, means)

Arguments

params	SplatPopParams object containing parameters for population scale simulations. See SplatPopParams for details.
means	Mean gene expression matrix with eQTL effects.

Value

matrix of quantile normalized gene mean expression levels.

Examples

if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
    requireNamespace("preprocessCore", quietly = TRUE)) {
    bulk.means <- mockBulkMatrix(n.genes = 100, n.samples = 100)
    bulk.qnorm <- splatPopQuantNorm(newSplatPopParams(), bulk.means)
}

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.