emptyRanges: Generate empty genomic ranges

Description Usage Arguments Value See Also Examples

View source: R/emptyRanges.R

Description

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

Usage

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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.

See Also

help("seqinfo", "GenomeInfoDb").

Examples

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

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

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

acidgenomics/freerange documentation built on July 19, 2019, 4:55 a.m.