Extensions

Full name SMRUCC.genomics.Model.Network.KEGG.ReactionNetwork.Extensions Assembly SMRUCC.genomics.Model.Network.KEGG Members 3

01 Syntax

SMRUCC.genomics.Model.Network.KEGG.ReactionNetwork.Extensions

02 Methods

Name	Overloads	Summary
BuildModel	1	利用代谢反应的摘要数据构建出代谢物的互作网络
GetReactions	2	Pull out all of the pathway related reactions data

03 Members

method BuildModel #

BuildModel(IEnumerable(Of ReactionTable), IEnumerable(Of NamedValue(Of String)), Boolean, Dictionary(Of String, String()), Boolean, Boolean, Boolean, Boolean, Boolean, Boolean)

利用代谢反应的摘要数据构建出代谢物的互作网络

Parameters

Name	Type	Description
`br08901`	`IEnumerable(Of ReactionTable)`	Metabolic links which is represented via the kegg reaction model data. A metabolic network will be build based on this reaction data. (代谢反应数据)
`compounds`	`IEnumerable(Of NamedValue(Of String))`	KEGG化合物编号，`{kegg_id => compound name}`
`extended`	`Boolean`	是否对结果进行进一步的拓展，以获取得到一个连通性更加多的大网络？默认不进行拓展
`enzymes`	`Dictionary(Of String, String())`	`{KO => protein names}`
`enzymaticRelated`	`Boolean`	是否只使用酶促反应进行网络的构建
`filterByEnzymes`	`Boolean`	Just re-construct a kegg metabolic network which its all reaction is related with the input enzymes list? (是否只使用enzymes的KO编号相关的反应来构建代谢网络)
`enzymeBridged`	`Boolean`	This option will affects the network connected style: true: compound -- enzyme -- compound false: compound -- compound set this parameter value to TRUE could create a metabolic network that used for run multiple omics data analysis.

method GetReactions overload 2 #

GetReactions(Map, Dictionary(Of String, ReactionTable()), Boolean)

Pull out all of the pathway related reactions data

Remarks

we are not going to add the non-enzymics reaction into each pathway map because this operation will caused all of the pathway map contains the similar compound profile which is bring by all of the non-enzymics reactions.

Parameters

Name	Type	Description
`pathway`	`Map`	-
`reactions`	`Dictionary(Of String, ReactionTable())`	A repository for the kegg reaction data models

method GetReactions #

GetReactions(Pathway, Dictionary(Of String, ReactionTable()), Boolean)

Pull out all of the pathway related reactions data

Remarks

Parameters

Name	Type	Description
`pathway`	`Pathway`	-
`reactions`	`Dictionary(Of String, ReactionTable())`	A repository for the kegg reaction data models