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GeneInfo

Prints detailed information on single genes. The information includes expression values and optional annotation.

Version 1.0
Bundle microarray
Categories Latex
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R
Source files component.xml GeneInfo.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr1 LogMatrix Mandatory Expression matrix 1.
expr2 LogMatrix Optional Expression matrix 2.
expr3 LogMatrix Optional Expression matrix 3.
geneAnnotation AnnotationTable Optional Annotation for the genes. The columns specified with the parameter annotationColumns are copied in the report.
groups SampleGroupTable Optional Sample group table that is used to fetch the human-readable name for sample groups. If not given, the group ID is used instead in the report.

Outputs

Name Type Description
report Latex Latex section that contains one section for each gene.

Parameters

Name Type Default Description
annotationColumns string "" Comma-separated list of column names in geneAnnotation that are copied into the report.
exprColumns string "*" Expression column names to be included. The special value * includes all columns.
geneConversionColumn string "" Column name in geneAnnotation that is used to convert reported gene names.
geneIDs string (no default) Comma-separated list of gene/probe IDs that refer to the ID column of the expression matrix.

Test cases

Test case Parameters IN
expr1
IN
expr2
IN
expr3
IN
geneAnnotation
IN
groups
OUT
report
case1 properties expr1 expr2 (missing) geneAnnotation groups (missing)

geneIDs=P1,P3,P4,
annotationColumns=GeneName,Description,
geneConversionColumn=GeneName


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