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Generate visualization for genes of interest with spliced isoforms.

Version 1.0
Bundle microarray
Categories Meap
Authors Ping Chen (ping.chen@helsinki.fi)
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Requires R ; meap (R-package)
Source files component.xml MeapVisualizer.r
Usage Example with default values


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.


Name Type Description
report HTML A visualization report with HTML format.


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
case1 properties expr geneList dbConnect sample report


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