Up: Component summary
Up: Component summary
Component
DEGReportCreates a LaTeX report on differentially expressed genes (DEGs). The report has two parts: a summary section that lists the number of over- and underexpressed genes in each sample group; and a gene list section that lists all the gene names. The latter usually goes to appendix.
| Version | 1.1.1 |
|---|---|
| Bundle | microarray |
| Categories | DEG Latex |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml DEGReport.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| deg | SetList | Mandatory | Sets of differentially expressed genes. If expression values are given (expr), there must be an annotation column SampleGroup that binds the set to an expression column. |
| geneAnnotation | AnnotationTable | Mandatory | Annotation for genes. Must contain the column named by geneColumn. |
| expr | Matrix | Optional | Expression values. Used to sort gene lists. |
Outputs| Name | Type | Description |
|---|---|---|
| summary | Latex | Summary section that lists the number of over- and underexpressed genes in each sample. |
| genelist | Latex | Gene list section that lists all the gene names. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| columns | int | 4 | Number of columns in gene list table. |
| geneColumn | string | "GeneName" | Column name in geneAnnotation that contains gene names. If empty, gene names are not printed. |
| sectionTitle | string | "Summary of differentially expressed genes" | Title for a new latex section. If none is given, a new section is not created. |
| sectionType | string | "section" | Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty. |
| setPattern | string | "" | R regular expression for matching set names. If empty, all sets are included. |
Test cases| Test case | Parameters▼ | IN deg |
IN geneAnnotation |
IN expr |
OUT summary |
OUT genelist |
|---|---|---|---|---|---|---|
| case1 | properties | deg | geneAnnotation | expr | summary | genelist |
|
setPattern=.*_(over|under) |
||||||
| case2_nogroup | (missing) | deg | geneAnnotation | expr | (expecting failure) | (expecting failure) |
| case3_no_expr | (missing) | deg | geneAnnotation | (missing) | summary | genelist |