get_permutations: Helper Function to generate shuffled means

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Helper Function to generate shuffled means

Description

Helper Function to generate shuffled means

Usage

get_permutations(
  lr_res,
  sce,
  nperms = 1000,
  seed = 1234,
  parallelize = FALSE,
  workers = 4,
  assay.type = "logcounts",
  verbose = TRUE
)

Arguments

lr_res	liana_pipe results
sce	SingleCellExperiment Object
nperms	number of permutations
seed	number used to set random seed
parallelize	logical whether to parallelize
workers	Number of workers to be used in parallelization
assay.type	- the type of data to be used to calculate the means (logcounts by default), available options are: "counts" and "logcounts"
verbose	logical for verbosity

Details

This function could be made generalizable to any set of genes, depending on the set (currently lr_res genes) that is used to filter - i.e. it could be replaced with e.g. genes from TF regulons

Value

Returns a list of shuffled gene means by cluster

saezlab/liana documentation built on Aug. 10, 2024, 8:14 a.m.