Up: Component summary
Up: Component summary
Component
RegionReportGenerates statistics about the DNA regions. The statistics include a length distribution and the frequencies of regions for each chromosome.
| Version | 1.1 |
|---|---|
| Bundle | microarray |
| Categories | Latex Short-read Sequencing |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml RegionReport.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| regions | CSV | Mandatory | List of genome regions |
| chromosomes | CSV | Optional | Table of chromosomes (row names) and their lengths in base pairs |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Statistics report |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| chrColumn | string | "chr" | Name of the chromosome column in input |
| endColumn | string | "end" | Name of the start locus column in input |
| lengthColumn | string | "length" | Name of the length column in chromosomes input |
| sectionType | string | "subsection" | Latex definition for the section level |
| startColumn | string | "start" | Name of the start locus column in input |
| title | string | "DNA region" | Name of the DNA region set |
Test cases| Test case | Parameters▼ | IN regions |
IN chromosomes |
OUT report |
||
|---|---|---|---|---|---|---|
| case1 | (missing) | regions | (missing) | report | ||
| case2 | properties | regions | chromosomes | report | ||
|
title = DNA region report, |
||||||
| case3_empty | properties | regions | (missing) | report | ||
|
title = An empty file |
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