/celltypes450

adjust for cell-type composition in 450K data using houseman's and other methods.

Primary LanguageRBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Adjust for cell composition in 450K data.

Much of the adjust.beta code was originally written by Andres Houseman. I have only put it into a simple to use function and packaged it.

Installation

> library(devtools)
> install_github("brentp/celltypes450")

About

See this thread for details.

Compared to minfi, which normalizes the sorted data with the new data:

comparison

To get your beta (0, 1) values adjusted for cell-type composition, use:

library(devtools)
install_github("brentp/celltypes450")
library(celltypes450)
adjusted = adjust.beta(beta)

To get the cell-composition estimates such as those from the image above:

cell.types = adjust.beta(beta, est.only=TRUE)