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

Description Usage Arguments See Also

View source: R/coor2index.R

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

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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 Nov. 9, 2018, 5:38 p.m.