R/convert_unit.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

####################################################################
## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
####################################################################

# Function to get a scaling factor such that positions may be converted from unit2 to unit1:

## Input:
### unit1: unit that we want to convert to
### unit2: unit that should be converted

## Output:
### factor: a scaling factor used in conversion of positions

## Required by:
### addChromlines
### adjustSeg
### plotGamma
### chromMax
### getx
### plotIdeogram
### getGlobal.xlim

## Requires:
# none

convert.unit <- function(unit1, unit2) {
  factor <- NA
  # Allowed units:
  units <- c("bp", "kbp", "mbp")

  if (identical(unit1, unit2)) {
    factor <- 1
  } else {
    if (identical(unit1, units[3])) {
      if (identical(unit2, units[2])) {
        factor <- 1 / (10^3)
      } else {
        if (identical(unit2, units[1])) {
          factor <- 1 / (10^6)
        }
      }
    } else {
      if (identical(unit1, units[2])) {
        if (identical(unit2, units[3])) {
          factor <- 10^3
        } else {
          if (identical(unit2, units[1])) {
            factor <- 1 / (10^3)
          }
        }
      } else {
        if (identical(unit1, units[1])) {
          if (identical(unit2, units[3])) {
            factor <- 10^6
          } else {
            if (identical(unit2, units[2])) {
              factor <- 10^3
            }
          }
        }
      }
    }
  }

  if (is.na(factor)) {
    if (all(units != unit1)) {
      stop("plot.unit must be one of 'kbp' and 'mbp'", call. = FALSE)
    }
  }

  return(factor)
} # end convert.unit