Matchmaking: Run Matchmaker

In stevexniu/scMatchmaker: Single Cell Matchmaker

Run Matchmaker

Description

Run matchmaker to Identify cell-cell interactions.

Usage

Matchmaking(
  object,
  ident1 = NULL,
  ident2 = NULL,
  stats = c("mean", "median"),
  pair.fxn = c("+", "*"),
  emd = FALSE,
  nbins = 100,
  n_perm = 100,
  weighted = FALSE,
  p.adjust.method = "none",
  min_emd_pct = 0,
  max_emd_pct = 1,
  drop_zero = FALSE,
  cutoff.stats = NA,
  save.perm = FALSE,
  n_cores = NULL,
  seed = 1
)

Arguments

object	Matchmaker object.
ident1	Cell type identity group 1. Default is NULL and all cell types will be used.
ident2	Cell type identity group 2. Default is NULL and all cell types will be used.
stats	Statistics used to calculate strength. mean, using mean (Default). medain, using median.
pair.fxn	Functions used to calculate pair strength. +, using sum of the pairs (Default). *, using product of the pairs.
emd	Whethter to run Earth Mover's Distance adjustment. Default is FALSE.
nbins	Number of bins to use for Earth Mover's Distance calculation. Default is 100.
n_perm	Number of random permutations. Default is 100.
weighted	Logic, compute weighted Earth Mover's Distance which will give higher weight/penalty on lowly expressed genes. Default is FALSE.
p.adjust.method	p value adjustment method. Default is "none". See details p.adjust.
min_emd_pct	Earth Mover's Distance below this percentile will be replaced with this percentile value. Default is 0.
max_emd_pct	Earth Mover's Distance above this percentile will be replaced with this percentile value. Default is 1.
drop_zero	Whether to drop all the zeros in the data when calculating EMD. Default is FALSE.
cutoff.stats	Cutoff used to calculate the statistics (mean or median). Default is NA. If set to 0, all 0 values will be removed when calculating mean or median.
save.perm	Whether to save permutation result. Default is FALSE.
n_cores	Number of cores used. Default is to use all cores - 1. See details makeCluster.
seed	Random seed number for permutation. Default is 1.

Value

Returns a Matchmaker object.

Examples

## Not run: 
object <- Matchmaking(object, stats = "mean", emd = TRUE, n_perm = 100)

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.