emptyRanges: Generate empty genomic ranges

In acidgenomics/r-acidgenomes: Acid Genomics Genome Annotations

Generate empty genomic ranges

Description

Utility function that provides support for creating internal GRanges for transgene and FASTA spike-in sequences.

Usage

emptyRanges(
  names,
  seqname = c("unknown", "transgene", "spike"),
  mcolnames = NULL
)

Arguments

names	character. Gene or transcript names.
seqname	character(1). Name of the alternative chromosome to be defined in seqnames where these ranges will be grouped. Defaults to "unknown" but "transgene" (transgenes) and "spike" (spike-ins) are also supported.
mcolnames	character or NULL. Metadata column names to be defined in the mcols of the GRanges return. Normally this does not need to be defined; useful when combining with another GRanges that contains metadata.

Value

GRanges.

Note

Updated 2019-08-21.

See Also

help("seqinfo", "GenomeInfoDb").

Examples

## Unknown/dead genes.
emptyRanges("ENSG00000000000", seqname = "unknown")

## Transgenes.
emptyRanges(c("EGFP", "TDTOMATO", "GAL4"), seqname = "transgene")

## Spike-ins.
emptyRanges("ERCC", seqname = "spike")

acidgenomics/r-acidgenomes documentation built on Jan. 12, 2024, 4:06 a.m.