Find cis SNPs around a set of Variable Methylated Regions (VMRs)

Identification of genotyped Single Nucleotide Polymorphisms (SNPs) close to each VMR using a distance threshold.

Usage

findCisSNPs(VMRs_df, genotype_information, distance = 1e+06)

VMRs_df: A GRanges object converted to a data frame. Must contain the following columns: "seqnames", "start", "end". These columns are present automatically when doing the object conversion and correspond to the chromosome number, and range of the region.
genotype_information: A data frame with information about genotyped sites of interest. It must contain the following columns: "CHROM" - chromosome number, "POS" - Genomic basepair position of SNP in the corresponding chromosome (must contain values of class int), and "ID" - SNP ID. The nomenclature of CHROM must match with the one used in the VMRs_df seqnames column (i.e., if VMRs_df$seqnames uses 1, 2, 3, X, Y or Chr1, Chr2, Chr3, ChrX, ChrY, etc. as chromosome number, the genotype_information$CHROM values must be encoded in the same way).
distance: The distance threshold to be used to identify cis SNPs. Default is 1 Mb.

A VMR_df object (a data frame compatible with GRanges conversion) with the following new columns:

The cis SNPs identified for each VMR, the number of SNPs surrounding each VMR in the specified window
VMR_index, which is created if not already existing based on the rownames of the VMR_df.

Important: please make sure that the positions of the VMR data frame and the ones in the genotype information are from the same genome build.