cpg_annotate

A small R script to provide quick annotation and gene lists for series of IlmnID's (450k probes). Currently working on a version to include support for 850k arrays.

Note: There is a hg38 updated slimmed down annotation file available for the 850k array (IlluminaEPIC_annotation_hg38.RDS).

example usage

Either clone or download this repository, ensure the Ilmn450K_anno.RDS file is in the same directory as the R script (cpg_annotate.R).

This has currently been tested on Linux, but should work on any system with R installed.

Rscript cpg_annotate.R reinius_beta_CD8T.txt

Note: the above text file reinius_beta_CD8T.txt has been included in this repository for testing purposes.

other bed files

Added a selection of potential useful bed files that were generated during the development of this script.

• added original bed file for 450k probes lifted over to hg38 with dbSNP info
• added a custom bed of hg38 UCSC gene symbols
• created a bed which intersects the above two files generating a hg38 version with UCSC genes (hg38), rather than the original hg19 UCSC genes from the Illimina annotation. Build process:
  • bedmap --echo --echo-map-id-uniq illumina450k_annotation_cpgsnps_hg38_all_sorted.bed ucsc_genes/hg38_ucsc_all_refgenes_sorted.bed | tr '|' '\t' > illumina450k_annotation_cpgsnps_hg38_ucscgenes_sorted.bed
  • bgzip illumina450k_annotation_cpgsnps_hg38_ucscgenes_sorted.bed
  • tabix illumina450k_annotation_cpgsnps_hg38_ucscgenes_sorted.bed.gz

To do

• add Illumina EPIC 850k annotation
• modify cpg_annotate to work for both 450k and 850k
• add hg38 position and SNP information to annotation file
• add UCSC hg38 referecnce gene symbols from custom bed
• add exit before further evaluation if no file is provided
• further tidy up script