Up: Component summary Component

ExtractCond

Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file. For example, colouring normal vs. tumor and normal vs. tumor subtypes.

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

Inputs

Name Type Mandatory Description
exprMatrix CSV Mandatory Normalized (and log-transformed) expression matrix to make MDS plot with. Should not have NA values.
reference CSV Mandatory List of input raw fastq files with Treatment (groups) information. Same format as input of smallRNAprep.

Outputs

Name Type Description
table CSV Sample group table.

Test cases

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

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