Up: Component summary Component


Wraps the SPP R package from http://compbio.med.harvard.edu/Supplements/ChIP-seq/ published in Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. Biotech. doi:10.1038/nbt.1508

Version 1.0
Bundle sequencing
Authors Lauri Lyly (lauri.lyly@helsinki.fi)
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Requires R ; SPP 1.10 (R-package)
Source files component.xml SPP.r
Usage Example with default values


Name Type Mandatory Description
treatment BinaryFile Mandatory Sample CSV file, with fields: chromosome name, region middle position, strand (either 1 for forward or 2 for reverse)
control BinaryFile Mandatory Control CSV file with similar format as treatment file.


Name Type Description
peaks CSV Called peaks regions ...


Name Type Default Description
bin int 5 bin tags within the specified number of basepairs to speed up calculation
fdr float 0.01 Desired FDR.
srange_max int 500
srange_min int 50

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