Description Usage Arguments Value See Also Examples
Extract features as "GRanges"
objects.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)
## S4 method for signature 'gbFeature'
ranges(x, join = FALSE, key = TRUE,
include = "none", exclude = "", ...)
## S4 method for signature 'gbFeatureTable'
ranges(x, join = FALSE, key = TRUE,
include = "none", exclude = "", ...)
## S4 method for signature 'gbRecord'
ranges(x, join = FALSE, key = TRUE, include = "none",
exclude = "", ...)
## S4 method for signature 'gbRecordList'
ranges(x, join = FALSE, key = TRUE,
include = "none", exclude = "", ...)
|
x |
A |
join |
Join compound genomic locations into a single range. |
key |
Include feature keys with ranges. |
include |
Include qualifiers as metadata columns. Can be "none", "all", or a character vector of qualifier tags. |
exclude |
Exclude specific qualifiers. |
... |
Further arguments passed to methods. |
A GRanges
or GRangesList
object.
start
, end
, span
, strand
,
location
, key
, qualif
1 2 3 4 5 6 7 8 9 10 | load(system.file("extdata", "marine_metagenome.rda", package = "biofiles"))
## default "GRanges" object.
ranges(x)
## subset CDSs and include "product", "note", "protein_id" as metadata.
ranges(x["CDS"], include = c("product", "note", "protein_id"))
## subset CDSs and exclude "translation"
ranges(x["CDS"], include = "all", exclude = "translation")
|
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