data.frame2GRanges: data.frame2GRanges

In RnBeads: RnBeads

Description

Converts a data.frame that defines genomic regions to object of type GRanges.

Usage

data.frame2GRanges(
  dframe,
  ids = rownames(dframe),
  chrom.column = "Chromosome",
  start.column = "Start",
  end.column = "End",
  strand.column = NULL,
  assembly = "hg19",
  sort.result = TRUE
)

Arguments

dframe	Table defining genomic regions.
ids	Region names (identifiers) as a character vector, or NULL if no names are present.
chrom.column	Column name or index that lists the chromosome names.
start.column	Column name or index that lists the start positions of the regions.
end.column	Column name or index that lists the end positions of the regions.
strand.column	Column name or index that lists the strands on which the regions are located. Set this to NULL if this region set is not strand-specific.
assembly	Genome assembly of interest. See rnb.get.assemblies for the list of supported genomes.
sort.result	Should the resulting table be sorted

Value

GRanges object encapsulating all well defined regions on supported chromosomes, contained in dframe. Columns other that the ones listed as parameters in this function are included as metadata.

Author(s)

Yassen Assenov

RnBeads documentation built on March 3, 2021, 2 a.m.