Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies

Data corresponding to the paper "Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies."
    
Corresponding scripts can be found at: https://github.com/pjhop/dnamarray_crossreactivity
All downstream analyses in c9_analysis.Rmd and in supplementary_note.Rmd can be reproduced using the deposited data as follows:

• Clone the dnamarray_crossreactivity repository: < git clone  https://github.com/pjhop/dnamarray_crossreactivity.git >
• Download the data ('data.zip') and place it in the 'dnamarray_crossreactivity' folder.
• Unzip the data.zip folder

Scripts used to generate the data in each subdirectory can be found at:

• data/processed/c9_matches/: https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches
• data/output/ewas/: https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas
• data/output/figs/: empty folder, running 'c9_analysis.Rmd' will save figures here.
• data/misc/: https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other
• data/extdata:
  • Zhou et al. annotations (EPIC.hg19.manifest.tsv.gz, HM450.hg19.manifest.pop.tsv.gz, HM450.hg19.manifest.tsv.gz) were downloaded from: https://zwdzwd.github.io/InfiniumAnnotation (downloaded at 17/09/2020)
  • Naeem et al. data (12864_2013_7006_MOESM2_ESM.csv) was downloaded from:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/
  • Chen et al. data (48639-non-specific-probes-Illumina450k.xlsx) was downloaded from  https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx
  • The anno_450k.txt.gz and anno_EPIC.txt.gz are subsets of the annotation files included in the following package respectively: https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html and https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html
•  data/genome_bs:  Scripts used to generate these data can be found at https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R and https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R .
•  data/raw: Individual-level data is available upon access at: https://ega-archive.org/studies/EGAS00001004587