granges_overlap: Find GenomicRanges overlap Find overlap genomic position...

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

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

Description

Find GenomicRanges overlap

Find overlap genomic position overlap between two GRanges objects.

Usage

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")

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.