Find GenomicRanges overlap Find overlap genomic position overlap between two GRanges objects.

Source: R/granges_overlap.R

Find GenomicRanges overlap

Find overlap genomic position overlap between two GRanges objects.

granges_overlap(
  dat1,
  dat2,
  chrom_col.1 = "chrom",
  start_col.1 = "start",
  end_col.1 = start_col.1,
  chrom_col.2 = "chrom",
  start_col.2 = "start",
  end_col.2 = end_col.2,
  return_merged = TRUE,
  unique_only = TRUE,
  style = "NCBI",
  verbose = FALSE
)

Arguments

dat1

Dataset 1 (can be GRanges or data.table).

dat2

Dataset 2. (can be GRanges or data.table).

chrom_col.1

Name of the chromosome column in dat1.

start_col.1

Name of the start position column in dat1.

end_col.1

Name of the end position column in dat2.

chrom_col.2

Name of the chromosome column in dat2.

start_col.2

Name of the start position column in dat2.

end_col.2

Name of the end position column in dat2.

return_merged

Whether to return an object with columns from dat1 and dat2 merged.

unique_only

Only return unique rows.

style

GRanges style (e.g. "NCBI, "UCSC") set by seqlevelsStyle.

verbose

Print messages.

Examples

dat1 <- echodata::BST1
dat2 <- echoannot::xgr_example
GenomicRanges::mcols(dat2) <- NULL

gr.hits <- echoannot::granges_overlap(dat1 = dat1, 
                                      dat2 = dat2, 
                                      chrom_col.1 = "CHR",
                                      start_col.1 = "POS")
#> Converting dat to GRanges object.
#> 778 query SNP(s) detected with reference overlap.