Converting single cells to pseudo-bulks.

pseudoBulk(
  sce,
  phenotypes = NULL,
  response = NULL,
  clusterid = NULL,
  assayName = "counts",
  resampSizes = 100,
  proportion = NULL,
  calcMean = FALSE,
  nPool = 15,
  seed = 904800
)

Arguments

sce: SingleCellExpeirment object.
phenotypes: Phenotypes to predict. Can be multiple.
response: Response matrix. Can be continuous.
clusterid: Column name of colData for specifying groups for pseudobulking.
assayName: Assay used for pseudobulking.
resampSizes: How many pseudo-bulk resamples to generate from each cluster.
proportion: Used to determine unequal resampSizes.
calcMean: Logical. Calculate mean of sum of expression for pseudobulking.
nPool: How many cells to use for pseudobulking.
seed: Random seeds

Value

An updated SingleCellExpeirment object with a pseudobulk assay.