Issue with ewas

[sngiam88]

Issue: When the ewas tool is used with Illumina 450K data, CpGs are unnecessarily dropped from output due to the annotation using IlluminaHumanMethylationEPICanno.ilm10b4.hg19 (i.e. those CpGs that are on the 450K array but not on the EPIC array).

See code here: https://github.com/RTIInternational/biocloud_docker_tools/blob/master/ewas/v0.0.2/ewas.R

Potential solution: If we want to continue supporting this tool, I would perhaps recommend that the user is required to input a parameter for which annotation package they want to use - since now there is 450K, EPIC & EPIC version 2 annotations available, I believe. And maybe an option for them to leave it "none" or null or something if they don't want annotation.