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

Description Usage Arguments

View source: R/coor2index.R

Description

convert continuous index to chromosome coordinates (reverse of coor2index)

Usage

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