removeCircularFeatures: NOT WORKING - Undo 'expandCircularFeatures' searches for...

In raim/segmenTools: Tools for Functional Genome Exploration

NOT WORKING - Undo expandCircularFeatures searches for circular features by the idTag added to ID and type columns in expandCircularFeatures, and maps downstream coordinates back to original features.

Description

NOT WORKING - Undo expandCircularFeatures searches for circular features by the idTag added to ID and type columns in expandCircularFeatures, and maps downstream coordinates back to original features.

Usage

removeCircularFeatures(
  features,
  coorCols = c("chr", "start", "end", "strand"),
  idTag = "-circ2",
  idCols = c(ID = "ID", type = "type", parent = "parent"),
  rmParent = TRUE
)

Arguments

features	list of genomic features with coordinates
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 chrL), start, end, and strand
idTag	tag used for tagging downstream halves
idCols	named vector of column names for feature ID, type, and feature parent; note that a "parent" column will be removed if it is (a) empty and (b) argument rmParent==TRUE
rmParent	rm the parent column

See Also

expandCircularFeatures

raim/segmenTools documentation built on May 5, 2024, 11:30 a.m.