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ExpressionSubset

Given an expression matrix and a CSV containing a subset of interest in one column (e.g. DEGs), extract a subset of the expression matrix containing just these genes of interest. Use, for example, as input to the HeatMapReport component.

Version 0.1
Bundle sequencing
Categories Expression smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi)
Issue tracker View/Report issues
Requires R
Source files component.xml ExpressionSubset.r
Usage Example with default values

Inputs

Name Type Mandatory Description
exprMatrix CSV Mandatory Expression matrix.
reference CSV Mandatory CSV file containing the subset of interest to filter from exprMatrix. Reference names should match that used in the exprMatrix.

Outputs

Name Type Description
subset CSV Expression matrix subset.

Parameters

Name Type Default Description
subsetColumn string "" Column name of subset file containing the reference names to match to the exprMatrix. If blank, the first column is used.

Test cases

Test case Parameters IN
exprMatrix
IN
reference
OUT
subset
case1 (missing) exprMatrix reference subset

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