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GOClustering

Clusters 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)
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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,
grayScale =false

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,
showClusterNames=false,
geneColumn=Gene

case5_pvalues properties goAnnotations expr (missing) (missing) (missing)

pvalues=true

case6_empty_input (missing) goAnnotations expr (missing) report clusters

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