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ExonExpression

Converts exon expression matrix for a list of exons of interest. If the initial input expression matrix is on probeset level, the component can combine the probeset level data into exon level data. If an exon has replicate probesets, the converted expression is "median", "mean", "max" or "min" of all its probesets.

Version 1.0
Bundle microarray
Categories Exon
Authors Ping Chen (ping.chen@helsinki.fi)
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Requires R ; meap (R-package)
Source files component.xml ExonExpression.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr LogMatrix Mandatory Probeset expression matrix from AffyReader.
sample SampleGroupTable Mandatory Samples used in pipeline. The table contains columns GroupID(key), Type(one of mean,median),SourceGroups(comma-separated list of sample IDs) and Description.
exon CSV Mandatory A list of exons of interest.

Outputs

Name Type Description
ExonExpr LogMatrix Converted exon expression matrix.

Parameters

Name Type Default Description
CombineType string "medianpolish" Type of method to combine expression of multiple probesets of each exon. "medianpolish","median", "mean", "min" and "max" can be used. When 'exprType' is 'exon', this parameter is not taken into considered in actural computing.
ExonColumn int 1 The index of column containing exon Ensembl ID in the input exon file.
ShowUnmatched boolean false A boolean parameter shows if the expression value of those input exons with matched results should be include in the ExonExpr matrix. If 'true', the expression of those exons is set to -1.
annotation string "/opt/sandbox/pchen/MEAPAnnotation_Human_v64" The path of exon array annotation file.

Test cases

Test case Parameters IN
expr
IN
sample
IN
exon
OUT
ExonExpr
case1 properties expr sample exon ExonExpr

CombineType=medianpolish,
ExonColumn=1,
ShowUnmatched=false,
metadata.timeout=0,


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