findInteractions: Calculate the Interaction Strength

In stevexniu/scMatchmaker: Single Cell Matchmaker

Calculate the Interaction Strength

Description

Calculate the interaction strength and statistical significance using random permutation tests.

Usage

findInteractions(
  data,
  idents,
  ligand,
  receptor,
  stats = c("mean", "median"),
  pair.fxn = c("+", "*"),
  n_perm = 100,
  emd = FALSE,
  nbins = 100,
  weighted = TRUE,
  p.adjust.method = "none",
  threshold = 0,
  min_pct = 0,
  max_pct = 1,
  drop_zero = FALSE,
  cutoff.stats = NA,
  return.perm = FALSE,
  n_cores = NULL,
  seed = 1
)

Arguments

data	Expression data. A d x M matrix with d rows of features and M columns of data points (cells).
idents	Cell type identity in characters or factors.
ligand	Name or index for ligand.
receptor	Name or index for receptor.
stats	Method 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.
n_perm	Number of random permutations. Default is 100.
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 10.
weighted	Logic, compute weighted Earth Mover's Distance which will give higher weight/penalty on lowly expressed genes. Default is TRUE.
p.adjust.method	p value adjustment method. Default is "none". See details p.adjust.
threshold	Threshold used for interaction products. See details calcStrength.
min_pct	Earth Movre's Distance values below this percentile will be replaced with this percentile value. Default is 0.
max_pct	Earth Movre's Distance Values 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.
return.perm	Whether to return the 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 list contains interaction strength and pvalues, optionally the null strength and Earth Mover's Distance similarity.

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