Component: GeneCount

GeneCount

Produces a LaTeX report that shows the number of genes or features under analysis in various phases of an Anduril script. One or two numbers are reported for each defined expression matrix. First, the number of features is the number of rows in an expression matrix, after filtering missing values. Second, the number of distinct genes is computed if the geneAnnotation table is given. Each row is mapped to a gene ID and the number of unique gene IDs is reported.

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 GeneCount.r
Usage	Example with default values GeneCount( expr1 = LogMatrix, //expr2 = LogMatrix, //expr3 = LogMatrix, //expr4 = LogMatrix, //expr5 = LogMatrix, //expr6 = LogMatrix, //expr7 = LogMatrix, //expr8 = LogMatrix, //geneAnnotation = AnnotationTable, geneColumn = "", minColumns1 = 0, minColumns2 = 0, minColumns3 = 0, minColumns4 = 0, minColumns5 = 0, minColumns6 = 0, minColumns7 = 0, minColumns8 = 0, title1 = "Expression values 1", title2 = "Expression values 2", title3 = "Expression values 3", title4 = "Expression values 4", title5 = "Expression values 5", title6 = "Expression values 6", title7 = "Expression values 7", title8 = "Expression values 8" )

Version

1.0

Bundle

microarray

Categories

Latex

Authors

Kristian Ovaska (kristian.ovaska@helsinki.fi)

Issue tracker

View/Report issues

Requires

Source files

component.xml GeneCount.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.
expr4	LogMatrix	Optional	Expression matrix 4.
expr5	LogMatrix	Optional	Expression matrix 5.
expr6	LogMatrix	Optional	Expression matrix 6.
expr7	LogMatrix	Optional	Expression matrix 7.
expr8	LogMatrix	Optional	Expression matrix 8.
geneAnnotation	AnnotationTable	Optional	If given, gene IDs for each row in expression matrices are retrieved from here and the number of distinct genes is included in the report.

Name

Type

Mandatory

Description

expr1

LogMatrix

Mandatory

Expression matrix 1.

expr2

LogMatrix

Optional

Expression matrix 2.

expr3

LogMatrix

Optional

Expression matrix 3.

expr4

LogMatrix

Optional

Expression matrix 4.

expr5

LogMatrix

Optional

Expression matrix 5.

expr6

LogMatrix

Optional

Expression matrix 6.

expr7

LogMatrix

Optional

Expression matrix 7.

expr8

LogMatrix

Optional

Expression matrix 8.

geneAnnotation

AnnotationTable

Optional

If given, gene IDs for each row in expression matrices are retrieved from here and the number of distinct genes is included in the report.

Name	Type	Description
report	Latex	LaTeX table that contains the number of features and genes for each defined expression matrix.

Name

Type

Description

report

Latex

LaTeX table that contains the number of features and genes for each defined expression matrix.

Parameters

Name	Type	Default	Description
geneColumn	string	""	Name of the column in geneAnnotation that is used to retrieve gene identifier. This value must be provided if geneAnnotation is present; otherwise, the value may be empty.
minColumns1	int	0	For expr1, only those rows that have non-missing values in at least minColumns1 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns2	int	0	For expr2, only those rows that have non-missing values in at least minColumns2 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns3	int	0	For expr3, only those rows that have non-missing values in at least minColumns3 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns4	int	0	For expr4, only those rows that have non-missing values in at least minColumns4 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns5	int	0	For expr5, only those rows that have non-missing values in at least minColumns5 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns6	int	0	For expr6, only those rows that have non-missing values in at least minColumns6 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns7	int	0	For expr7, only those rows that have non-missing values in at least minColumns1 columns are counted. Rows that have more than this number of missing values are filtered before counting.
minColumns8	int	0	For expr8, only those rows that have non-missing values in at least minColumns8 columns are counted. Rows that have more than this number of missing values are filtered before counting.
title1	string	"Expression values 1"	A description of expression matrix expr1 that is shown in the report.
title2	string	"Expression values 2"	A description of expression matrix expr2 that is shown in the report.
title3	string	"Expression values 3"	A description of expression matrix expr3 that is shown in the report.
title4	string	"Expression values 4"	A description of expression matrix expr4 that is shown in the report.
title5	string	"Expression values 5"	A description of expression matrix expr5 that is shown in the report.
title6	string	"Expression values 6"	A description of expression matrix expr6 that is shown in the report.
title7	string	"Expression values 7"	A description of expression matrix expr7 that is shown in the report.
title8	string	"Expression values 8"	A description of expression matrix expr8 that is shown in the report.

Name

Type

Default

Description

geneColumn

string

Name of the column in geneAnnotation that is used to retrieve gene identifier. This value must be provided if geneAnnotation is present; otherwise, the value may be empty.

minColumns1

int

For expr1, only those rows that have non-missing values in at least minColumns1 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns2

int

For expr2, only those rows that have non-missing values in at least minColumns2 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns3

int

For expr3, only those rows that have non-missing values in at least minColumns3 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns4

int

For expr4, only those rows that have non-missing values in at least minColumns4 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns5

int

For expr5, only those rows that have non-missing values in at least minColumns5 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns6

int

For expr6, only those rows that have non-missing values in at least minColumns6 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns7

int

For expr7, only those rows that have non-missing values in at least minColumns1 columns are counted. Rows that have more than this number of missing values are filtered before counting.

minColumns8

int

For expr8, only those rows that have non-missing values in at least minColumns8 columns are counted. Rows that have more than this number of missing values are filtered before counting.

title1

string

"Expression values 1"

A description of expression matrix expr1 that is shown in the report.

title2

string

"Expression values 2"

A description of expression matrix expr2 that is shown in the report.

title3

string

"Expression values 3"

A description of expression matrix expr3 that is shown in the report.

title4

string

"Expression values 4"

A description of expression matrix expr4 that is shown in the report.

title5

string

"Expression values 5"

A description of expression matrix expr5 that is shown in the report.

title6

string

"Expression values 6"

A description of expression matrix expr6 that is shown in the report.

title7

string

"Expression values 7"

A description of expression matrix expr7 that is shown in the report.

title8

string

"Expression values 8"

A description of expression matrix expr8 that is shown in the report.

Test cases

Test case	Parameters▼	IN expr1	IN expr2	IN expr3	IN expr4	IN expr5	IN expr6	IN expr7	IN expr8	IN geneAnnotation	OUT report
case1	properties	expr1	expr2	expr3	expr4	(missing)	(missing)	(missing)	(missing)	(missing)	report
	minColumns1=0, title1=Title 1, minColumns2=1, title2=Title 2, minColumns3=2, title3=Title 3, minColumns4=2, title4=Title 4
case2-anntable	properties	expr1	expr2	expr3	expr4	(missing)	(missing)	(missing)	(missing)	geneAnnotation	report
	minColumns1=0, title1=Title 1, minColumns2=1, title2=Title 2, minColumns3=2, title3=Title 3, minColumns4=2, title4=Title 4, geneColumn=Gene

Test case

Parameters▼

IN
expr1

IN
expr2

IN
expr3

IN
expr4

IN
expr5

IN
expr6

IN
expr7

IN
expr8

IN
geneAnnotation

OUT
report

case1

(missing)

minColumns1=0,
title1=Title 1,
minColumns2=1,
title2=Title 2,
minColumns3=2,
title3=Title 3,
minColumns4=2,
title4=Title 4

case2-anntable

(missing)

minColumns1=0,
title1=Title 1,
minColumns2=1,
title2=Title 2,
minColumns3=2,
title3=Title 3,
minColumns4=2,
title4=Title 4,
geneColumn=Gene

Anduril

GeneCount

Inputs

Outputs

Parameters

Test cases