Up: Component summary
Up: Component summary
Component
DEE2DEGFind differentially expressed genes (DEG) based on differentially expressed exons (DEE).
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Exon |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; meap (R-package) |
| Source files | component.xml DEE2DEG.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| dee | CSV | Mandatory | Differentially expressed exons with statistical test p-value or fold change |
| dbConnect | CSV | Mandatory | Database connection properties with host name, database, user name and password. |
Outputs| Name | Type | Description |
|---|---|---|
| deg | CSV | Differentially expressed genes with scores. It lists merged p-value, fold change (FC), the number of DEEs, the number of total exons and scores (0-1). |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ExonColumn | string | "" | The column name of Exon ID. |
| cutoff | float | 0.2 | If a gene has a specified percentage of exons that were identified as DEEs, the gene is selected as a DEG. |
| sigColumn | string | "" | The column name of significant values for ranking. If 'base' is 'rank-fc', 'sigColumn' should be fold change values. If 'base' is 'rank-pvalue', it should be p values. |
Test cases| Test case | Parameters▼ | IN dee |
IN dbConnect |
OUT deg |
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|---|---|---|---|---|---|---|
| case1 | properties | dee | dbConnect | deg | ||
|
ExonColumn=ExonID, |
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