parseKaryo: Parses a karyotype-like formula
In cghRA: Array CGH Data Analysis and Visualization

Description Usage Arguments Value Author(s) See Also Examples

This function produces a cghRA.regions object from a simplified karyotype formula, associating copy numbers to numeric coordinates.

1 2	parseKaryo(formula, bandTrack, name = as.character(NA), design = NULL, alteratedOnly = TRUE)

`formula`	Single character value, the formula to be parsed. See 'Examples'.
`bandTrack`	A `track.table` object with cytoband definition, as returned by the `track.UCSC_bands` function from the `Rgb` package.
`name`	Single character value, to be used as name for the produced object.
`design`	A `cghRA.design` object, or `NULL`. If provided, a `cghRA.copies` object will be produced, using `design` to compute probe content of each region. Else, a `track.table` object will be returned.
`alteratedOnly`	Single logical value, if `TRUE` normal clones (2n without alteration) will not be averaged with alterated clones for the final copy amount computation. If all clones are normals, a normal genome will be returned anyway.

Returns a list with two elements : "clones" and "copies".

"clones" is a summary of the clones found in the formula as an integer value, with mitosis counts as values and ploidy as names.

"copies" is a track.table-inheriting object with genomic regions of distinct copy numbers. If design is provided, the object is a cghRA.copies object, else a track.table object.

Sylvain Mareschal

cghRA.copies

  ## Not run: 
    karyo <- paste(
      "111<5n>,6(1qt-p11),4(1p11-pt),4(2),8(3),4(4),6(5),6(6pt-q22),6(6q26-qt),",
      "2(6q22-q26),6(7pt-q31),3(7q31-qt),6(9),4(10),4(11),4(12),6(13),4(14),",
      "4(15pt-q22),2(15q22-qt),2(16),4(17),6(18),4(19),4(21),4(22) [6] ; 46<2n> [7]",
      collapse = ""
    )
    parseKaryo(karyo, bandTrack)
  
## End(Not run)