splatPopEstimate {splatter} | R Documentation |
Estimate simulation parameters for the eQTL population simulation from real data. See the individual estimation functions for more details on how this is done.
splatPopEstimate( counts = NULL, means = NULL, eqtl = NULL, params = newSplatPopParams() )
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 |
SplatPopParams object containing the estimated parameters.
splatPopEstimateEffectSize
,
splatPopEstimateMeanCV
if (requireNamespace("VariantAnnotation", quietly = TRUE) && requireNamespace("preprocessCore", quietly = TRUE)) { # Load example data library(scater) sce <- mockSCE() params <- splatPopEstimate(sce) }