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Up: Component summary
Component
GOClusteringClusters genes based on their gene ontology (GO) annotations. Distances between the GO terms are weighted with their informativiness. The component produces a hierarchical clustering and a heatmap visualization that shows the gene expressions. This is a simple example output.
The csbl.go R package is available at http://csbi.ltdk.helsinki.fi/csbl.go/.
| Version | 1.1.3 |
|---|---|
| Bundle | microarray |
| Categories | Clustering GO |
| Authors | Ping Chen (ping.chen@helsinki.fi), Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI), Erkka Valo (erkka.valo@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; csbl.go (R-package) |
| Source files | component.xml GOClustering.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| goAnnotations | AnnotationTable | Mandatory | GO annotations for the genes |
| expr | LogMatrix | Optional | Gene expressions |
| similarityTable | CSV | Optional | Custom GO probability table that is used in similarity computation. If this is not given, a built-in table for a given organism is used (see the parameter organism). |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Latex subsection containing the go clustering plots. |
| clusters | SetList | Cluster members in a list of sets where set ID is the name of the cluster. The cluster members are listed using the key column in the GO annotation table. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ColumnWidth | float | 15 | Control the column width of the GO MEMBER table. |
| asBitmap | boolean | false | Produce heatmap in Portable network graphics (PNG) format instead of Portable document format (PDF). PNG bitmaps are more suitable if the heatmap contains large number of samples and genes. |
| columnMargin | float | 5 | Margin for column names in heatmap |
| cutLimit | float | 0.5 | Clustering cut off height for the hierachical clustering of the genes. This limit is between 0 and 1, where 0 refers to more specific groups. |
| decimal | int | 3 | Control the output of long decimal. |
| drawHeatmap | boolean | true | If true, draw a heatmap. |
| dropUnknown | boolean | false | Genes with no GO annotations are excluded if this flag is true |
| geneColumn | string | "" | Name of the gene name column in the annotation file. The value is used for creating the report. The given column is used for listing all the members in the clusters to the report. If the value is empty, cluster member lists are not put into the report. |
| goColumn | string | "GO" | Name of the GO annotation column in the annotation file |
| grayScale | boolean | true | If true, heatmap is in grayscale. If false, heatmap is colorful. |
| heatmapScale | string | "row" | Determines how the values for the heatmap are scaled. Legal values are "row", "column" and "none". This corresponds to the scale parameter of the R function heatmap. |
| organism | int | 9606 | NCBI taxonomy ID for the organism whose gene set is used for GO probabilities. This is used if the input similarityTable is not given. Supported organisms: Homo sapiens: 9606, Saccharomyces cerevisiae: 4932, Caenorhabditis elegans: 6239, Drosophila melanogaster: 7227, Mus musculus: 10090, Rattus norvegicus: 10116. |
| pvalues | boolean | false | If true, compute p-values for information contents of the clusters using a permutation test. The p-values are shown in their own table in the report. The permutation test may be slow. |
| rowMargin | float | 5 | Margin for row names in heatmap |
| sectionType | string | "subsection" | Type of LaTeX section: usually one of section, subsection
or subsubsection. No section statement is written if
sectionTitle is an empty string. |
| showClusterNames | boolean | true | If true, show cluster names G1, ..., Gn on the right side of the heat map. If false, show gene names. |
| title | string | "GO clustering" | Title for the subsection and for the heatmap image. |
| xLab | string | "Samples" | Label for the x-axis of the heatmap |
| yLab | string | "GO.groups" | Label for the y-axis of the heatmap |
Test cases| Test case | Parameters▼ | IN goAnnotations |
IN expr |
IN similarityTable |
OUT report |
OUT clusters |
|---|---|---|---|---|---|---|
| case1 | properties | goAnnotations | expr | (missing) | (missing) | (missing) |
|
dropUnknown=true, |
||||||
| case2_onecolumn | (missing) | goAnnotations | expr | (missing) | report | (missing) |
| case3 | (missing) | goAnnotations | (missing) | (missing) | (missing) | (missing) |
| case4_known_output | properties | goAnnotations | expr | (missing) | report | clusters |
|
grayScale=true, |
||||||
| case5_pvalues | properties | goAnnotations | expr | (missing) | (missing) | (missing) |
|
pvalues=true |
||||||
| case6_empty_input | (missing) | goAnnotations | expr | (missing) | report | clusters |