compute.matrix: Compute Matrix

In RicUIB/AligNet: Tool to Analyze PPI Networks and Align Networks using AligNet Algorithm algorithm

Description

Compute several matrices

Usage

compute.matrix(net1, net2 = NULL, type = "Distance", mode = "Similarity",
  database = NULL, database2 = NULL, byComp = TRUE, normalized = TRUE)

Arguments

net1	an igraph object
net2	an igraph object for modes BLAST and FC if Net2 is not NULL, computes the matrix between nodes in Net1 and Net2.
type	what matrice do you want to compute (BLAST, DSD, Distance, FC, Degree)
mode	for type BLAST : pident or bitscore. For DSD and Distance distance, similarity or similarity by components. For FC the list of ontologies
database	for BLAST and FC the database which proteins belongs.
database2	for BLAST and FC the database which proteins belongs.
byComp	for DSD and Distance if the similarity or distance must be normalized by components
normalized	if the matrix will be normalized

Value

The matrix

RicUIB/AligNet documentation built on May 28, 2019, 2:27 p.m.