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GeneTable

Compiles gene ID sets into CSV files that contain gene annotations and expression. This is useful for compiling microarray results into result files. There is one CSV file for each gene set.

Version 1.1.1
Bundle microarray
Categories Latex
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R
Source files component.xml GeneTable.r
Usage Example with default values

Inputs

Name Type Mandatory Description
idlist SetList Mandatory Sets of IDs of interest (e.g., differentially expressed genes). There should be an annotation column SampleGroup that binds each gene set to a sample group in expr or groups.
expr LogMatrix Optional Expression data
geneAnnotation AnnotationTable Optional Annotation for genes. The parameter annotationColumns gives the names of the columns that are used from this table. Additionally, idConvertColumn may refer to this table.
groups SampleGroupTable Optional The idlist may contain sample groups that are composed of several individual samples. This input provides names of the individual samples. The expression matrix contains expression values for the individual samples, each of which is included in output.
sampleAnnotation CSV Optional If given, columns from this table are included in the result CSV files. Column names are given with the parameter sampleAnnotationColumns. The first column contains sample group IDs and the second contains gene IDs.

Outputs

Name Type Description
out CSVList CSV tables for sample groups. There is one file for each ID list in "idlist". The first column is an ID column.

Parameters

Name Type Default Description
allowMissingExpr boolean true If true, allow genes that are present in the SetList but not in expression. If false, signal error for such genes.
annotationColumns string "*" Column names in geneAnnotation that are included in the result. The special value * includes all columns except the first (ID) column.
columnOrder string "expr,geneAnnotation,sampleAnnotation" Order of entries in the result files. The parameter contains a comma-separated list of values "expr", "geneAnnotation" and "sampleAnnotation" in some order. For example, if "expr" is the first entry, then expression columns are written first. The orders within annotation columns are specified using annotationColumns and sampleAnnotationColumns.
expressionLabel string "Expression" Label for expression column(s).
groupID string "" If the SetList input does not contain a SampleGroup column, this specifies the default sample group ID.
idConvertColumn string "" If non-empty, gene/probe IDs are converted using this column. If empty, IDs are printed as they are in the input deg.
sampleAnnotationColumns string "*" Column names in sampleAnnotation that are included in the result. The special value * includes all columns except the two first (ID) columns.
setPattern string "" R regular expression for matching set names. If empty, all sets are included.
sortColumn string "" If non-empty, this is a column name in the final result that is used to sort each CSV result file. In non-empty, expression values are used for sorting, if present.

Test cases

Test case Parameters IN
idlist
IN
expr
IN
geneAnnotation
IN
groups
IN
sampleAnnotation
OUT
out
case1 properties idlist expr geneAnnotation (missing) (missing) out

setPattern=.*-(over|under),
idConvertColumn=Agilent,
annotationColumns=GeneName,Description,
expressionLabel=Fold change

case2 properties idlist expr geneAnnotation (missing) sampleAnnotation out

setPattern=.*-(over|under),
idConvertColumn=Agilent,
annotationColumns=GeneName,Description,
sampleAnnotationColumns=pvalue,
expressionLabel=Fold change

case3_groups properties idlist expr geneAnnotation groups (missing) out

setPattern=.*-(over|under),
idConvertColumn=Agilent,
annotationColumns=GeneName,Description,
expressionLabel=Fold change

case4_order properties idlist expr geneAnnotation (missing) sampleAnnotation out

setPattern=.*-(over|under),
idConvertColumn=Agilent,
annotationColumns=GeneName,Description,
sampleAnnotationColumns=pvalue,
expressionLabel=Fold change,
columnOrder=sampleAnnotation,geneAnnotation,expr,
sortColumn=pvalue


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