Estimate simulation parameters for the eQTL population simulation from real data. See the individual estimation functions for more details on how this is done.
Usage
splatPopEstimate(
counts = NULL,
means = NULL,
eqtl = NULL,
params = newSplatPopParams()
)Arguments
- counts
either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
- means
Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population.
- eqtl
data.frame with all or top eQTL pairs from a real eQTL analysis. Must include columns: 'gene_id', 'pval_nominal', and 'slope'.
- params
SplatPopParams object containing parameters for the simulation of the mean expression levels for the population. See
SplatPopParamsfor details.
Examples
if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
requireNamespace("preprocessCore", quietly = TRUE)) {
# Load example data
library(scuttle)
sce <- mockSCE()
params <- splatPopEstimate(sce)
}
#> NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.