dtToGr: Converts a data.table (DT) object to a GenomicRanges (GR)...

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Converts a data.table (DT) object to a GenomicRanges (GR) object. Tries to be intelligent, guessing chr and start, but you have to supply end or other columns if you want them to be carried into the GR.

Description

Converts a data.table (DT) object to a GenomicRanges (GR) object. Tries to be intelligent, guessing chr and start, but you have to supply end or other columns if you want them to be carried into the GR.

Usage

dtToGr(
  DT,
  chr = "chr",
  start = "start",
  end = NA,
  strand = NA,
  name = NA,
  splitFactor = NA,
  metaCols = NA
)

Arguments

DT	A data.table representing genomic regions.
chr	A string representing the chromosome column.
start	A string representing the name of the start column.
end	A string representing the name of the end column.
strand	A string representing the name of the strand column.
name	A string representing the name of the name column.
splitFactor	A string representing the name of the column to use to split the data.table into multiple data.tables.
metaCols	A string representing the name of the metadata column(s) to include in the returned GRanges object.

Value

A GRanges object.

Examples

start1 = c(seq(from=1, to = 2001, by = 1000), 800)
chrString1 = c(rep("chr1", 3), "chr2")
dt = data.table::data.table(chr=chrString1,
                            start=start1,
                            end=start1 + 250)
newGR = dtToGr(dt)                

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.