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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

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.

Outputs

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.

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


Generated 2018-12-11 07:42:06 by Anduril 2.0.0