nuget
需要程序处于联网状态
PathwayMapping
01 Syntax
SMRUCC.genomics.Assembly.KEGG.WebServices.PathwayMapping
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| Reconstruct | 2 | KEGG Mapper – Reconstruct Pathway > http://www.genome.jp/kegg/tool/map_pathway.html Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome anno… |
| ColorPathway | 1 | Search&Color Pathway is an advanced version of the KEGG pathway mapping tool, where given objects (genes, proteins, compounds, glycans, reactions, drugs, etc.) are searched again… |
| GetKOlist | 1 | |
| KOCatalog | 3 | KEGG直系同源分类统计 |
| DefaultKOTable | 1 | Build default from BriteHText.Load_ko00001() |
| CustomPathwayTable | 1 | http://www.kegg.jp/kegg-bin/get_htext?ko00001.keg |
| ShowEnrichmentPathway | 1 | url can be encoding by URLEncoder |
03 Fields
| Name | Overloads | Summary |
|---|---|---|
| KEGG_show_pathway | 1 |
04 Members
Reconstruct(
IEnumerable(Of NamedValue(Of String)), Boolean, String)KEGG Mapper – Reconstruct Pathway
Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO) identifiers or K numbers. Each line of the gene list contains the user-defined gene identifier followed by, if any, the assigned K number. The mapping is performed through the K numbers against the KEGG reference pathways.
Parameters
| Name | Type | Description |
|---|---|---|
list$ | IEnumerable(Of NamedValue(Of String)) | Enter gene list with KO annotation(line format: |
globalmap | Boolean | Include global/overview maps |
Reconstruct(
String, Boolean, String)KEGG Mapper – Reconstruct Pathway
Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO) identifiers or K numbers. Each line of the gene list contains the user-defined gene identifier followed by, if any, the assigned K number. The mapping is performed through the K numbers against the KEGG reference pathways.
Parameters
| Name | Type | Description |
|---|---|---|
list$ | String | Enter gene list with KO annotation |
globalmap | Boolean | Include global/overview maps |
ColorPathway(
String, Boolean, Boolean, Boolean, Boolean, String)Search&Color Pathway is an advanced version of the KEGG pathway mapping tool, where given objects (genes, proteins, compounds, glycans, reactions, drugs, etc.) are searched against KEGG pathway maps and found objects are marked in any background and foreground colors (bgcolor and fgcolor). The objects in different types of pathway maps are specified by the following KEGG identifiers and aliases.
Parameters
| Name | Type | Description |
|---|---|---|
list$ | String | - |
work$ | Boolean | - |
GetKOlist(
IEnumerable(Of String), String)Parameters
| Name | Type | Description |
|---|---|---|
geneIDs | IEnumerable(Of String) | - |
DIR$ | String | 文件夹之中存放着以基因号为文件名的OrthologRESTXml |
KOCatalog(
IEnumerable(Of NamedValue(Of String)), Dictionary(Of String, BriteHText))KEGG直系同源分类统计
Parameters
| Name | Type | Description |
|---|---|---|
KO_maps | IEnumerable(Of NamedValue(Of String)) |
|
KOCatalog(
IEnumerable(Of NamedValue(Of String)))KEGG直系同源分类统计
Parameters
| Name | Type | Description |
|---|---|---|
KO_maps | IEnumerable(Of NamedValue(Of String)) |
|
KOCatalog(
IEnumerable(Of NamedValue(Of String)), String)Custom KO classification set can be download from: http://www.kegg.jp/kegg-bin/get_htext?ko00001.keg. You can replace the %s mark Using kegg organism code In url example As: http://www.kegg.jp/kegg-bin/download_htext?htext=%s00001&format=htext&filedir= for download the custom KO classification set.
Parameters
| Name | Type | Description |
|---|---|---|
KO_maps | IEnumerable(Of NamedValue(Of String)) | - |
ko00001$ | String | User custom classification database |
DefaultKOTable
Build default from BriteHText.Load_ko00001()
CustomPathwayTable(
String)Parameters
| Name | Type | Description |
|---|---|---|
ko00001$ | String | - |
ShowEnrichmentPathway(
String, String)url can be encoding by URLEncoder
Parameters
KEGG_show_pathway