how to get genomic locations of Sequence patterns in R

Question

[Alewa]

Hi, my current implementation returns the indexes of input genomic range where "CG" are found but i want to get the genomic location matching the pattern. pls see code and example data. thank you in advance for your help

getMotif_sites <- function(ref_genome=NULL, grList=NULL, context="CG"){
        library(Biostrings)
  # Load ref genome of choice 
  genome_pkg <- switch(ref_genome,
                   mm10 = "BSgenome.Mmusculus.UCSC.mm10",
                   hg38 = "BSgenome.Hsapiens.UCSC.hg38",
                   stop("Invalid ref_genome specified")
  )

    # Load the actual genome data
    library(genome_pkg, character.only = TRUE)
    genome_data <- get(genome_pkg)


#get seq of the granges in question x=grList[[1]]
    seqGrList <- lapply(grList, function(x) {
        # print(seqnames(x))
        seqGr <- getSeq(genome_data, x) #get seqs from ref genome
        motif_locations <- Biostrings::vmatchPattern(context, seqGr) #get cpg sites


        # Calculate the starts based on the ends and the width
ends <- motif_locations@ends[[1]]
width <- nchar(context)
starts <- ends - width + 1

# Convert to GRanges
        gr <- GRanges(seqnames = seqnames(x),
                      ranges = IRanges(start = starts, end = ends))

        })

        return(GRangesList(seqGrList))
}

data

>dput(gr)
new("GRanges", seqnames = new("Rle", values = structure(1L, levels = "chr1", class = "factor"), 
    lengths = 1L, elementMetadata = NULL, metadata = list()), 
    ranges = new("IRanges", start = 177728813L, width = 2000L, 
        NAMES = NULL, elementType = "ANY", elementMetadata = NULL, 
        metadata = list()), strand = new("Rle", values = structure(3L, levels = c("+", 
    "-", "*"), class = "factor"), lengths = 1L, elementMetadata = NULL, 
        metadata = list()), seqinfo = new("Seqinfo", seqnames = "chr1", 
        seqlengths = NA_integer_, is_circular = NA, genome = NA_character_), 
    elementMetadata = new("DFrame", rownames = NULL, nrows = 1L, 
        elementType = "ANY", elementMetadata = NULL, metadata = list(), 
        listData = structure(list(), names = character(0))), 
    elementType = "ANY", metadata = list())