byComplex: Evaluate protein co-membership within cellular organizational...

In SLGI: Synthetic Lethal Genetic Interaction

Description

Count the protein co-members of one (or more) cellular organizational units such as complex(es). This co-membership can be characterized by a synthetic lethal interaction if bpL is the list of observed synthetic lethal interactions or it can be characterized by the number of all the expected interactions within that complexes if bpL is all the interactions tested.

Usage

byComplex(bpL,interactome)

Arguments

bpL	List of tested genes (or reported as synthetic lethal) per bait.
interactome	Adjacency matrix where the rows are the genes and the columns represent the cellular organizational units, e.g., ScISI

Value

Vector of the number of genes(proteins) co-member in one or more biological complexes or pathways.

Author(s)

N. LeMeur and R. Gentleman

See Also

withinComplex

Examples

  data(ScISIC)
  data(AtongPair)
  pairSL <-  AtongPair[ AtongPair[,3],]
  SLlist <- split(as.character(pairSL[,2]),as.character(pairSL[,1]))
  ##Number of synthetic lethal pairs within the same complexe 
  bySL <-byComplex(SLlist, ScISIC)
 

SLGI documentation built on Nov. 8, 2020, 11 p.m.