df2gr: Convert data frame to GRanges

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Convert data frame to GRanges

Description

Convert a data frame of genomic coordinates to GRanges.

Usage

df2gr(
  x,
  seq = "chr",
  start = "start",
  end = "end",
  strand = NULL,
  si = NULL,
  keep.all.seqlevels = FALSE,
  names2use = "row"
)

Arguments

x	data frame of genomic coordinates
seq	name of the column containing the sequence of the intervals
start	name of the column containing the start of the intervals
end	name of the column containing the end of the intervals
strand	name of the column containing the strand of the intervals
si	output from the "seqinfo" function from the GenomeInfoDb package
keep.all.seqlevels	if TRUE, all sequence levels from si are kept, otherwise, only those present in x
names2use	if NULL, the output will have no names; if "row", it will have the row names of the input (if any); else, it will have the content of the specified column (if it exists)

Value

GRanges

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.