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

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

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