Component: GeneTable

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 GeneTable( idlist = SetList, //expr = LogMatrix, //geneAnnotation = AnnotationTable, //groups = SampleGroupTable, //sampleAnnotation = CSV, allowMissingExpr = true, annotationColumns = "", columnOrder = "expr,geneAnnotation,sampleAnnotation", expressionLabel = "Expression", groupID = "", idConvertColumn = "", sampleAnnotationColumns = "", setPattern = "", sortColumn = "" )

Version

1.1.1

Bundle

microarray

Categories

Latex

Authors

Kristian Ovaska (kristian.ovaska@helsinki.fi)

Issue tracker

View/Report issues

Requires

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.

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.

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.

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.

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

Test case

Parameters▼

IN
idlist

IN
expr

IN
geneAnnotation

IN
groups

IN
sampleAnnotation

OUT
out

case1

(missing)

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

case2

(missing)

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

case3_groups

(missing)

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

case4_order

(missing)

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

Anduril

GeneTable

Inputs

Outputs

Parameters

Test cases