How to find CpGs within a certain distance from a gene of interest?

Question

[sswang25]

I am very new to bioinfromatics and have never handled DNA methylation data before. I have Illumina EPIC array data and I am looking for specific CpG probes that are within 2.5 megabases from the start of specific genes of interest. I am most interested in CpG probes in the promoter regions of my genes of interest. I want to create a list of these CpG probes based on their location and only use them to test for differentially methylated probes between my two groups of patients.

I have no idea how to do this, so any help would be really helpful.

[sswang25]

I managed to get the chromosome number and the start position and end position of all of my genes of interest:

I have the Chromosome number and MAPINFO i.e. location of my CpG sites:

How do I go about finding out which CpG probes are situated within the start/end positions of the genes I have identified? I can't figure out how to code this selection in R as the chromosome column has to match and the MAPINFO value I assume has to between the start and end values.

[Basti]

Create two Granges objects corresponding to your gene coordinates and the probes : Beware, first you need to transform your chromosome columns to "chr1" "chr2" ... and not "1" "2" "3" After this,

probesRanges = GRanges(seqnames=probes$CHR,ranges=IRanges(start=probes$MAPINFO,end=probes$MAPINFO+1))
genesRanges = GRanges(seqnames=genes$CHR,ranges=IRanges(start=genes$MAPINFO,end=genes$MAPINFO+1))

Then, use the findOverlaps() function from GenomicAlignments package : findOverlaps(probesRanges,genesRanges)

Answer 1

[Basti]

You can start by listing the coordinates of the regions you are interested in on genome assembly hg19. Then you download the Illumina EPIC annotation file from bioconductor :

library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
data("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
data(Locations)
locEPIC=data.frame(Locations)

Finally you just have to retrieve the coordinates of the CpGs that are located within the list of coordinates of genes of interest you identified

[sswang25]

Hi thank you very much. So in essence I make a dataframe from genomic ranges of the areas of the genome I'm interested in. Using the dataframe I can get the CpG probe names in these regions from the Epic manifest?

Is there a way to find out which CpG probes are in Cpg Islands, promoter regions etc from the Epic manifest?

[Basti]

Yes this is how I would do the selection. For annotation, there are several available but I personally use it via the ChAMP package :

library(ChAMP)
data(probe.features.epic)

[sswang25]

Thanks very much! I will try both these solutions out