Up: Component summary
Up: Component summary
Component
MeapVisualizerGenerate visualization for genes of interest with spliced isoforms.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Meap |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; meap (R-package) |
| Source files | component.xml MeapVisualizer.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr | LogMatrix | Mandatory | Exon expression matrix from MeapExpression component. |
| geneList | CSV | Mandatory | A CSV file contains a column of gene Ensembl IDs. |
| dbConnect | CSV | Mandatory | Database configuration file stores database connect details. |
| sample | SampleGroupTable | Mandatory | A sample group table for grouping samples into "Group1" and "Group2" for comparison. |
Outputs| Name | Type | Description |
|---|---|---|
| report | HTML | A visualization report with HTML format. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| HeatColNum | int | 100 | The number of colors (>= 1) to be in the palette. |
| NProcess | int | 1 | The number of processes are invoked in parallel execution. |
| SigType | string | "both" | A string specifies if t-test or fold change should be done. It can be one of 'pvalue', 'fc' and 'both'. |
| alternative | string | "two.sided" | A character string specifying the alternative hypothesis, must be one of "two.sided", "greater" or "less". |
| downCol | string | "green" | Color to use for lowest values. |
| geneColumn | int | 1 | The column index of gene Ensembl IDs in input 'geneList' file. |
| geneFilter | boolean | true | Filter genes without transcript expression. |
| metaData | string | "." | The directory for storing meta data. The meta data will be removed after the execution. |
| paired | boolean | false | A boolean for pairwise t-test. The default is "FALSE". |
| species | string | "Homo_sapiens" | The species of exon array data in study. It surports 'Homo_sapiens', 'Mus_musculus' or 'Rattus_norvegicus'. |
| transcriptFilter | boolean | true | Filter transcripts in Ensembl database that do not pass the quality control. The default is 'TRUE'. |
| upCol | string | "red" | Color to use for highest values. |
Test cases| Test case | Parameters▼ | IN expr |
IN geneList |
IN dbConnect |
IN sample |
OUT report |
|---|---|---|---|---|---|---|
| case1 | properties | expr | geneList | dbConnect | sample | report |
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metadata.timeout=0 |
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