Cell count estimation - Githubissues

FoxoTech / methylcheck

Python-based Illumina methylation array quality control software.

MIT License

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Cell count estimation #5

Open brianchengithub opened 5 years ago

brianchengithub commented 5 years ago

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 commented 5 years ago

@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 commented 5 years ago

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.