Who’s Afraid of the X?

Incorporating the X and Y chromosomes into the analysis of DNA methylation microarray data

This repository contains code from Inkster et al. 2023, with exemplars for processing and analysis (differential DNAme testing) available in the file aCA_XY_Processing_Analysis.md.

Additional annotation files for the Illumina DNAme arrays indexing which CpG probes overlap repetitive elements, the X-transposed region, and cancer testis gene family members are also provided for both the 450K and EPIC arrays:

1. Annotation_XY_450.csv
2. Annotation_XY_850.csv

To download these annotations, click on the file and choose "Download" in the top right-hand corner, OR in R use:

git450loc <- https://github.com/amy-inkster/XY_Processing_Analysis/blob/main/Annotation_XY_450.csv
anno450 <- read.csv(git450loc)

Please direct any feedback or questions to Amy Inkster at amymichelleinkster (at) gmail.com