nuget
生成BIOM数据模型
BIOM
01 Syntax
SMRUCC.genomics.Analysis.Metagenome.BIOM
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| Imports | 2 | Imports sample matrix from biom file as OTU table data. |
| sparseMatrix | 1 | |
| EXPORT | 1 |
03 Members
Imports(
IEnumerable(Of Names), Int32, Int32, Boolean, String)按照OTU的序列数量进行降序排序之后，所取出来的OTU的数量，默认只截取前100个OTU
Parameters
| Name | Type | Description |
|---|---|---|
source | IEnumerable(Of Names) | - |
takes | Int32 | Reorder Names.numOfSeqs desc and then take top n otu for imports as biom data. |
cut | Int32 | Names.numOfSeqs should at least greater than this number cutoff value that will be imports as biom data. |
Imports(
BIOMDataSet(Of Double))Imports sample matrix from biom file as OTU table data.
Parameters
| Name | Type | Description |
|---|---|---|
biom | BIOMDataSet(Of Double) | - |
sparseMatrix(Names(),
Index(Of String))Parameters
| Name | Type | Description |
|---|---|---|
array | Names() | - |
nameIndex | Index(Of String) | The column name index |
EXPORT(
IEnumerable(Of OTUData(Of Double)), Boolean)Parameters
| Name | Type | Description |
|---|---|---|
table | IEnumerable(Of OTUData(Of Double)) | 因为丰度数据可能是0到1之间的，也可能是原始的序列数量，也可能是经过归一化的，所以在这里会需要进行归一化操作，归一化为0到100之间的数 |