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API Docs / SMRUCC.genomics.Core / Extensions

Extensions

Full name SMRUCC.genomics.Assembly.KEGG.Extensions Assembly SMRUCC.genomics.Core Members 12

01 Syntax

SMRUCC.genomics.Assembly.KEGG.Extensions

02 Methods

NameOverloadsSummary
GetIDpairedList 1 这个主要是应用于ID mapping操作的拓展函数
DirectGetChEBI 1 Example as: [ChEBI] 16810
IDlistStrings 1
ValidateEntryFormat 1 检测判断所输入的字符串是否是符合格式要求的？
TheSameAs 1 Example as: Same as: C00001
RemarksTable 1 将Remarks数据转换为字典对象
TheSameAs 1 得到和这个药物同义的KEGG代谢物编号, 返回来的字符串可能会包含有多个ID编号 例如C\d+和G\d+可能会同时出现
GetPathwayBrite 1 这个函数会自动将物种的KEGG前缀去除掉，从而能够直接匹配字典之中的键名
DoKeggProfiles 1
LevelAKOStatics 1

03 Fields

NameOverloadsSummary
KEGGCompoundIDPatterns 2 + C compound + D drug + G glycan

04 Members

method GetIDpairedList #
GetIDpairedList(String)

这个主要是应用于ID mapping操作的拓展函数

Parameters
NameTypeDescription
text$String

Example as the text data in the kegg drugs or kegg disease object:

 E2A-PBX1 (translocation) [HSA:6929 5087] [KO:K09063 K09355]
method DirectGetChEBI #
DirectGetChEBI(Compound)

Example as: [ChEBI] 16810

Parameters
NameTypeDescription
cpdCompound

-

method IDlistStrings #
IDlistStrings(String, String())
Parameters
NameTypeDescription
tag$String

-

list$String()

-

Returns

Example as:

 HSA:6929 5087
method ValidateEntryFormat #
ValidateEntryFormat(String)

检测判断所输入的字符串是否是符合格式要求的？

Parameters
NameTypeDescription
s$String

-

method TheSameAs #
TheSameAs(String())

Example as:

 Same as: C00001
Parameters
NameTypeDescription
s$String()

-

method RemarksTable #
RemarksTable``1(``0)

将Remarks数据转换为字典对象

Type Parameters
NameDescription
T
Parameters
NameTypeDescription
o``0

-

method TheSameAs #
TheSameAs``1(``0)

得到和这个药物同义的KEGG代谢物编号, 返回来的字符串可能会包含有多个ID编号 例如C\d+和G\d+可能会同时出现

Type Parameters
NameDescription
T
Parameters
NameTypeDescription
o``0

-

method GetPathwayBrite #
GetPathwayBrite(Dictionary(Of String, Pathway), String)

这个函数会自动将物种的KEGG前缀去除掉，从而能够直接匹配字典之中的键名

Parameters
NameTypeDescription
tableDictionary(Of String, Pathway)

-

ID$String

-

method DoKeggProfiles #
DoKeggProfiles(Dictionary(Of String, Double), Int32)
Parameters
NameTypeDescription
profilesDictionary(Of String, Double)

[kegg_pathwayMapId -> value]

displaysInt32

-

method LevelAKOStatics #
LevelAKOStatics(IEnumerable(Of NamedValue(Of String)), KOCatalog(), Boolean)
Parameters
NameTypeDescription
mappingsIEnumerable(Of NamedValue(Of String))

{geneID -> KO} mapping data collection.

keepsZEROKOCatalog()

默认不保存计数为零的分类

Returns

这个函数所返回去的数据一般是用作于绘图操作的

field KEGGCompoundIDPatterns #
KEGGCompoundIDPatterns
  • C compound
  • D drug
  • G glycan
field KEGGCompoundIDPatterns #
KEGGCompoundIDPatterns