A method for calling DMRs using Illumina 450K Methylation BeadChip arrays implemented as part of suite of functions in the Bioconductor package ChAMP – an all-in-one analysis pipeline that takes raw methylation data and derives MVPs and DMRs for further investigation. Probe Lasso is a flexible window based approach that gathers neighbouring significant-signals to define clear DMR boundaries for subsequent in-depth analysis. The principal motive for developing this algorithm is to redirect subsequent analysis away from just probes/regions located in promoters/CGIs, which the array is skewed toward and leverage information from putatively important, but largely ignored, intergenic regions.

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Probe Lasso specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Stability:
Stable

Publications

  • (Butcher and Beck, 2015) Probe Lasso: A novel method to rope in differentially methylated regions with 450K DNA methylation data. Methods.
    PMID: 25461817

Link to literature

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