FilterConnectome

Filters a connectomic edgelist output from CreateConnectome according to user inputs. Defaults are set to reasonable initial parameters for data clean-up and exploration.

FilterConnectome(
  connectome,
  min.pct = NULL,
  max.p = NULL,
  min.DOR = NULL,
  min.exp = NULL,
  min.z = NULL,
  modes.include = NULL,
  sources.include = NULL,
  targets.include = NULL,
  mechanisms.include = NULL,
  features = NULL,
  verbose = T,
  remove.na = F
)

Arguments

connectome	A connectomic edgelist output from CreateConnectome
min.pct	Minimum fraction of cells within a given cluster expressing the ligand or receptor.
max.p	Maximum p-value for ligand and receptor. Filtration on this column requires prior p-value calculation.
min.DOR	Minimum log-normalized Diagnostic Odds Ratio for the ligand or receptor for its cell type within an edge.
min.exp	Minimum normalized expression level of ligand and receptor.
min.z	Minimum z-score for ligand and receptor.
modes.include	String or vector signifying mode(s) of interest in include.
sources.include	Source nodes of interest. Output will be limited to edges coming from these sources.
targets.include	Target nodes of interest. Output will be limited to edges landing on these targets.
mechanisms.include	Ligand - Receptor pairs of interest. The character string should match entries in the 'pair' column of the connectome.
verbose	Whether to output feedback to user
remove.na	Whether to remove edges containing 'NA' (no mapping to original object - only useful if investigating orphan ligands and receptors)