Skip to contents

Generate empty genomic ranges

Source: R/emptyRanges.R
emptyRanges.Rd

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")
#> GRanges object with 1 range and 0 metadata columns:
#>                   seqnames    ranges strand
#>                      <Rle> <IRanges>  <Rle>
#>   ENSG00000000000  unknown     1-100      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

## Transgenes.
emptyRanges(c("EGFP", "TDTOMATO", "GAL4"), seqname = "transgene")
#> GRanges object with 3 ranges and 0 metadata columns:
#>             seqnames    ranges strand
#>                <Rle> <IRanges>  <Rle>
#>       EGFP transgene     1-100      *
#>   TDTOMATO transgene   101-200      *
#>       GAL4 transgene   201-300      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

## Spike-ins.
emptyRanges("ERCC", seqname = "spike")
#> GRanges object with 1 range and 0 metadata columns:
#>        seqnames    ranges strand
#>           <Rle> <IRanges>  <Rle>
#>   ERCC    spike     1-100      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths