getMultiLayerGraphIDs: retrieve multilayer interacted nodes for given IDs and...

In GeneAnswers: Integrated Interpretation of Genes

Description

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

Usage

getMultiLayerGraphIDs(graphIDs, idType=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction', 'Customized'), edgeM=NULL, layers=1, filterGraphIDs=NULL, filterLayer=0, UP=TRUE, directed=FALSE, verbose=TRUE)

Arguments

graphIDs	a character vector for given IDs
idType	type of IDs, could be one of 'GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction' and 'Customized'
edgeM	a 2-column Matrix representing a network
layers	an integer, specify how many layers will be retrieved.
filterGraphIDs	a chacater vector for filtered IDs
filterLayer	an integer, specify where filterGraphIDs are applied.
UP	logic, determine search Parents or Children. Only valid for directed relation.
directed	logic, the network is a directed or not
verbose	logic, specify to show information or not.

Details

Currently, if idType is 'GO', 'GO.BP', 'GO.CC' or 'GO.MF', edgeM will be ignore. 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 are applied only at the filterLayer and more outer layers. This means the nodes between the filterLayer layer and the most external layer belong to the filterGraphIDs. The nodes between given graphIDs and the (filterLayer-1) layer are or are not from filterGraphIDs, but those nodes not in filterGraphIDs should be able to be finally connected by given graphIDs and filterGraphIDs.

Value

return a list containing elements to represent a network. The first element is a logic value, TRUE means no more connection between the most external layer nodes and other nodes. The second element is a list of layer-length. If the 1st element is FASLE, the length of 2nd element should be (layers + 1). And starting from the 3rd elements, the remaining elements construct a network.

Author(s)

Gang Feng, Pan Du and Simon Lin

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

See Also

getSingleLayerGraphIDs

Examples

require(GeneAnswers)
example(GeneAnswers)
getMultiLayerGraphIDs(rownames(getEnrichmentInfo(x))[5:6], UP=FALSE)

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.