nuget
Create motif via the clustering of the blastn alignment result
MotifTree
01 Syntax
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.MotifTree
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| BuildTree | 1 | 使用!values字典键来获取目标位点上的所有mapping结果 |
| compares | 1 | 计算两个片段的overlap的区域的占比 |
| ExtractSites | 1 | |
| FilterMotifs | 2 | 可能会有多个家族的调控因子作用在该位点上 |
| FilterMotifsQuantile | 1 | 可能会有多个家族的调控因子作用在该位点上 |
03 Members
BuildTree(
IEnumerable(Of BlastnMapping))使用!values字典键来获取目标位点上的所有mapping结果
Parameters
| Name | Type | Description |
|---|---|---|
mappings | IEnumerable(Of BlastnMapping) | - |
compares(
Location, Location)计算两个片段的overlap的区域的占比
Parameters
| Name | Type | Description |
|---|---|---|
a | Location | - |
b | Location | - |
ExtractSites(
NaiveBinaryTree(Of Location, BlastnMapping))Parameters
| Name | Type | Description |
|---|---|---|
tree | NaiveBinaryTree(Of Location, BlastnMapping) | 因为当节点非常多的时候，直接使用二叉树的结构可能会因为很多层次的递归而造成stack overflow的问题 所以在这里直接使用AVLTree对象的ToArray来避免这种情况的出现 |
FilterMotifs(
IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())), Func(Of String, String), Func(Of String, String), Int32, Boolean)可能会有多个家族的调控因子作用在该位点上
Parameters
| Name | Type | Description |
|---|---|---|
sites | IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())) | - |
getFamily | Func(Of String, String) | - |
getTarget | Func(Of String, String) | - |
hits% | Int32 | - |
FilterMotifs(
IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())), Func(Of String, String), Func(Of String, String), String)可能会有多个家族的调控因子作用在该位点上
Parameters
| Name | Type | Description |
|---|---|---|
sites | IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())) | - |
getFamily | Func(Of String, String) | - |
getTarget | Func(Of String, String) | - |
hitsExpression | String | - |
FilterMotifsQuantile(
IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())), Func(Of String, String), Func(Of String, String), Double)可能会有多个家族的调控因子作用在该位点上
Parameters
| Name | Type | Description |
|---|---|---|
sites | IEnumerable(Of ValueTuple(Of NucleotideLocation, BlastnMapping())) | - |
getFamily | Func(Of String, String) | - |
getTarget | Func(Of String, String) | - |
quantile | Double | - |