Up: Component summary
Up: Component summary
Function
NovelExprMatrix
Take output of miRanalyzer (or miRDeep2) and create an expression matrix with the putative novel miRNAs found.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Expression Novel smallRNA |
| Specialties | generic |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| novelArray | Array<BinaryFile> | Mandatory | Output array where putative novel miRNA counts can be retrieved per sample. |
Outputs| Name | Type | Description |
|---|---|---|
| csv | CSV | Expression matrix of putative novel miRNA expression, merged across samples, with separate columns for coordinates (chromosome, start, end position, and strand). |
| csv_wID | CSV | Expression matrix of putative novel miRNA expression, merged across samples, with a single column of unique IDs based on coordinates. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| maxLength | int | 300 | Maximum allowed length of merged sequence regions. e.g. The maximum length of a miRNA precursor. |
| maxPointDistance | int | 30 | Merge the counts of neighbouring putative novel miRNA regions with this maximum (genomic) distance. Chromosome, start, and end positions are used in the calculations. |
| method | string | "miranalyzer" | Either "miranalyzer" or "mirdeep2" to distinguish what files and where in the files the putative novel miRNAs are written. |
| minPercent | float | 0 | Minimum percentage of samples that a putative novel miRNA should have counts in to be included in the expression matrix. |