coor2index: convert chromosome coordinates to continuous index
In raim/segmenTools: Tools for Functional Genome Exploration

coor2index

R Documentation

convert chromosome coordinates to continuous index

Description

convert chromosome coordinates to continuous index

Usage

coor2index(
  features,
  chrS,
  chrMap,
  cols = c("start", "end", "coor"),
  chrCol = "chr",
  strandCol = "strand",
  reverse = c("-", -1),
  circular = FALSE
)

Arguments

`features`	a table of chromosome features that must contain the chromosome number (option `chrCol`), one or more chromosome positions (option `cols`) and strand information (column `strandCol`).
`chrS`	the chromosome index, indicating the start position of each chromosome in the continuous index, derived from chromosome length information; simply the cumulative lengths of ordered chrosomes, see function `getChrSum`
`chrMap`	a vector of chromosome names using `features`' chromosome column, in the same order as `chrS`
`cols`	name of the columns giving coordinates that will be mapped to continuous index
`chrCol`	name of the column that gives the chromosome number
`strandCol`	name of the column that gives forward/reverse strand information
`reverse`	a vector of possible reverse strand indicators
`circular`	suppresses re-sorting to start < end for circular chromosomes