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DEE2DEG

Find differentially expressed genes (DEG) based on differentially expressed exons (DEE).

Version 1.0
Bundle microarray
Categories Exon
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires R ; meap (R-package)
Source files component.xml DEE2DEG.r
Usage Example with default values

Inputs

Name Type Mandatory Description
dee CSV Mandatory Differentially expressed exons with statistical test p-value or fold change
dbConnect CSV Mandatory Database connection properties with host name, database, user name and password.

Outputs

Name Type Description
deg CSV Differentially expressed genes with scores. It lists merged p-value, fold change (FC), the number of DEEs, the number of total exons and scores (0-1).

Parameters

Name Type Default Description
ExonColumn string "" The column name of Exon ID.
cutoff float 0.2 If a gene has a specified percentage of exons that were identified as DEEs, the gene is selected as a DEG.
sigColumn string "" The column name of significant values for ranking. If 'base' is 'rank-fc', 'sigColumn' should be fold change values. If 'base' is 'rank-pvalue', it should be p values.

Test cases

Test case Parameters IN
dee
IN
dbConnect
OUT
deg
case1 properties dee dbConnect deg

ExonColumn=ExonID,
sigColumn=pvalue,FC,
metadata.timeout=60


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