GeneAnswers (version 2.14.0)

getSingleLayerGraphIDs: retrieve direct interacted nodes for given IDs and interaction Matrix

Description

A function to retrieve direct interacted nodes for given IDs and interaction Matrix with specified filtered IDs.

Usage

getSingleLayerGraphIDs(graphIDs, edgeM, remove=TRUE, filterGraphIDs=NULL, directed=FALSE, UP=TRUE)

Arguments

graphIDs

a character vector for given IDs

edgeM

a 2-column Matrix representing connectionship

remove

logic, remove the non-connection graphIDs in the return values

filterGraphIDs

a chacater vector for filtered IDs

directed

logic, the network is a directed or not

UP

logic, determine search Parents or Children. Only valid for directed relation.

Value

return a list representing a network.

Details

edgeM is a 2-column matrix. For directional connection, the direction is from column 1 elements to column 2 elements. For non-directional connection, each connection should be reversely presented twice, one is from column 1 element to column 2 element, while another is from column 2 element to column 1 element. In other words, non-directional connection is considered as two reverse directional connections. filterGraphIDs is used to only keep nodes in filterGraphIDs.

References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

Examples

m <- matrix(c('1','4', '2', '6', '1', '5', '3', '7', '5', '2'), ncol=2, byrow=TRUE)
m
getSingleLayerGraphIDs(c('1','2','3'), m)

# if the connection is not directional, the connection between '5' and '2' will be missed without changing m.
m <- rbind(m, c('2', '5'))
getSingleLayerGraphIDs(c('1','2','3'), m)