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IlluminaAnnotator

Fetches genomic annotations for Illumina methylation and expression array probes.

Version 13.10
Bundle microarray
Categories Annotation
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Requires FDb.InfiniumMethylation.hg19 (R-bioconductor) ; IlluminaHumanMethylation27k.db (R-bioconductor) ; illuminaHumanv3.db (R-bioconductor) ; illuminaHumanv4.db (R-bioconductor)
Source files component.xml IlluminaAnnotator.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in CSV Mandatory A list of Illumina probe ids.

Outputs

Name Type Description
out CSV Table of annotations defined by 'types' for input probes.

Parameters

Name Type Default Description
arrayType string (no default) Array type. One of 'v4', '450' or '27'.
keyColumn string "" Name of column in 'csv' containing probe ids or an empty string for the first column.
targetDB string "ENSEMBL,SYMBOL" Comma-separated list annotation types. Possible values and their descriptions are listed here. Defaults to Ensembl GeneId and GeneName.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in out

arrayType = 450

case2 properties in out

arrayType = 450,
keyColumn = ProbeID,
targetDB = CHR,CHRLOC,CHRLOCEND

case3 properties in out

arrayType = v4


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