generateIntergenicCoor: Resolve and generate genic element coordinates from UCSC...

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Resolve and generate genic element coordinates from UCSC genePred table.

Description

Function generates intergenic coordinates from a UCSC genePred table. It allows users to specify the genePred data source, the relative position and minimum length for intergenic regions, and whether to return the results as a Coordinate object or a data.table.

Usage

generateIntergenicCoor(
  genepred,
  genome.name,
  fasta.path,
  igr.rel.pos = c(5000, 7500),
  igr.min.length = 150,
  return.coor.obj = FALSE
)

Arguments

genepred	UCSC genePred table or database name ("refseq" or "gencode").
genome.name	UCSC genome name (e.g., hg38, mm39).
fasta.path	Path to a directory of user-provided genome FASTA files or the destination to save the NCBI/UCSC downloaded reference genome files.
igr.rel.pos	Intergenic relative position, defaults to c(5000, 7500).
igr.min.length	Minimum length for intergenic regions, default is 150.
return.coor.obj	Return results as a Coordinate object? Default FALSE.

Value

Intergenic coordinates as a data.table or Coordinate object.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.