Up: Component summary
Up: Component summary
Component
ExtractCond
Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file. For example, colouring normal vs. tumor and normal vs. tumor subtypes.
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | Quality Control smallRNA |
| Authors | Katherine Icay (katherine.icay@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml extractCond.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| exprMatrix | CSV | Mandatory | Normalized (and log-transformed) expression matrix to make MDS plot with. Should not have NA values. |
| reference | CSV | Mandatory | List of input raw fastq files with Treatment (groups) information. Same format as input of smallRNAprep. |
Outputs| Name | Type | Description |
|---|---|---|
| table | CSV | Sample group table. |
Test cases| Test case | Parameters▼ | IN exprMatrix |
IN reference |
OUT table |
|---|---|---|---|---|
| case1 | (missing) | exprMatrix | reference | table |