Cell count estimation

[brianchengithub]

To compute cell counts based on DNA methylation data, use the 'estimateCellCounts' command in the 'minfi' Bioconductor package:

https://rdrr.io/bioc/minfi/man/estimateCellCounts.html

[nhrigby]

@brianchengithub FYI: This will require preprocessQuantile (default preprocessing method for blood and DLPFC samples), so I'm going to work on getting that in place first.
It also looks like this might depend on the convertArray function, so I might have to build that out too.

[marcmaxson]

• port over data robot linear model coefficients (randy)
• code them into a function (for a set of probes) (marc)
• add as another "probe filter" type step -- but this is analysis of samples based on a subset of probes -- in QC workflow
• support standard EPIC + 450k shared probe set.
• give randy the "shared probes" list (intersection)
• compare accuracy of this shared list vs other non-shared list.