Enhancer in ChAMPdata

Question

[Xiaofan]

Does anyone know what is the source of the enhancer annotation from the "probe.features" data in the "ChAMPdata" R package.

It seems this annotation file identifies many enhancers (102559 out of 485577 [21%] probes, see code below) even more than that expected from EPIC platform, which may only have ~30000 out of 850k probes (3.5%).

library(ChAMPdata)
data("probe.features")
table(probe.features$Enhancer)

TRUE 
102559

Many thanks in advanced.

Answer 1

[Yuan]

Hi Xiaofan:

The enhancer information was obtained from origin illumina manifest downloaded from here. I checked the enhancer column, which show the same number as yours.

I am not sure how initially the annotation was generated, but the enhancer is not used in whole ChAMP package.

Best Tian