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ExonAnnotator

Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface.

Version 1.0
Bundle microarray
Categories Exon Annotation
Authors Ping Chen (ping.chen@helsinki.fi), Riku Louhimo (Riku.Louhimo@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; RMySQL (R-package)
Source files component.xml ExonAnnotator.r
Usage Example with default values

Inputs

Name Type Mandatory Description
query CSV Mandatory Must contain the column named by the parameter 'KeyColumn' that contains query Ensembl gene, transcript or exon IDs.
dbConnect CSV Mandatory Database configuration file stores database connect details.

Outputs

Name Type Description
table CSV Result table contains mapped gene, transcript or exon Ensembl ID.

Parameters

Name Type Default Description
InputType string (no default) The type of query IDs. It can be one of 'Gene', 'Transcript' and 'Exon'.
KeyColumn string "" The name of column contains query Ensembl gene, transcript or exon IDs. Defaults to the first column of the input file.
TargetType string (no default) Comma separated list of target ID types. Supports 'Gene', 'Transcript' and 'Exon'.
large boolean false If the query is over 50000 IDs, set 'large' to 'true' to avert database connection error.

Test cases

Test case Parameters IN
query
IN
dbConnect
OUT
table
case1 properties query dbConnect table

KeyColumn=.ExonId,
InputType=Exon,
TargetType=Exon,Gene,Transcript

case2 properties query dbConnect table

KeyColumn=TranscriptID,
InputType=Transcript,
TargetType=Transcript,Exon

case3 properties query dbConnect table

InputType=Gene,
TargetType=Gene,Exon,
large=true


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