expandCircularFeatures | R Documentation |
Splits genome features that span start/end coordinates of circular
chromosomes, and adds the downstream half with optional modification
of ID, and type values. Circular features are recognized here by
start > end, in left->right direction of genome annotation.
Strand information MUST NOT BE ENCODED IN start/end coordinate direction,
but explicitly provided via a strand column!
Note that only the upstream half retains
all column information (exceptions: see argument copyCols
),
the downstream half will only carry information on coordinates, and
optionally updated feature type and ID.
The update will only happen if the passed table contains type and ID
information (see argument idCols
. The split can be reversed
by function removeCircularFeatures
.
expandCircularFeatures(
features,
chrL,
coorCols = c("chr", "start", "end", "strand"),
reverse = c("-", -1),
idTag = "-circ2",
idCols = c(ID = "ID", type = "type", parent = "parent"),
copyCols = FALSE,
insertRows = TRUE
)
features |
a list of genomic features with coordinates |
chrL |
obligatory list of chromosome lengths, in order used
in chromosome column in |
coorCols |
ordered string vector providing the column names
of coordinate columns to be used; must be of length 4 and provide in
order: chromosome number (refering to argument |
reverse |
allowed indicators of reverse strand features
in strand column (see argument |
idTag |
tag to add to downstream ID and type |
idCols |
named vector of column names for feature ID, type, and feature parent; note that a "parent" column will be added if not present to refer the downstream half to its upstream feature, which retains all other information |
copyCols |
copy values to circular feature copy; either logical
|
insertRows |
insert the circular features below their parent,
if set to |
removeCircularFeatures
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