index2coor: convert continuous index to chromosome coordinates (reverse...

In raim/segmenTools: Tools for Functional Genome Exploration

convert continuous index to chromosome coordinates (reverse of coor2index)

Description

convert continuous index to chromosome coordinates (reverse of coor2index)

Usage

index2coor(
  features,
  chrS,
  chrMap,
  cols = c("start", "end", "coor"),
  chrCol = "chr",
  strandCol = "strand",
  relCol,
  strands = c(1, -1)
)

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
chrMap	a vector of chromosome names, in the same order as chrS; if provided chromosome index will be mapped back to chromosome name
cols	names 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
relCol	relative position mapping left/right -> upstream/downstream, depending on strand
strands	forward/reverse strand indicators

raim/segmenTools documentation built on April 25, 2024, 10:14 a.m.