Run Matchmaker

Run matchmaker to Identify cell-cell interactions.

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

if (FALSE) {
object <- Matchmaking(object, stats = "mean", emd = TRUE, n_perm = 100)
}