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DEGReport

Creates 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)
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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

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