[BioC] Help on cghMCR units of gapAllowed

[Nathalie Conte]

HI,
 I just want a precision on cghMCR package for those familiar with it.
The function cghMCR will have an argument about gap allowed which will 
fuse segment of DNA below this size. What is the scale is it bp or Kb?In 
the manual, it seems quite clear that it is pb but in one example, it 
seems to be kb...
|segments| 	|segments| is a data frame extracted from the "output" 
element of the object returned by segment of the package DNAcopy or 
|getSegments 
<http://rss.acs.unt.edu/Rdoc/library/cghMCR/html/cghMCR-class.html>|
|gapAllowed| 	|gapAllowed| is an integer specifying low threshold of 
base pair number to separate two adjacent segments, belower which the 
two segments will be joined as an altered span
|alteredLow| 	|alteredLow| is a positive number between 0 and 1 
specifying the lower reshold percential value. Only segments with values 
falling below this threshold are considered as altered span
|alteredHigh| 	|alteredHigh| is a positive number between 0 and 1 
specifying the upper reshold percential value. Only segments with values 
falling over this threshold are considered as altered span
|recurrence| 	|recurrence| is an integer between 1 and 100 that 
specifies the rate of occurrence for a gain or loss that are observed 
across sample. Only gains/losses with ocurrence rate grater than the 
threshold values are declared as MCRs

example given by the manual, specify 500kb and this is written like 
this... should be 500 000 if the unit is bp

  require("cghMCR")
  data("sampleData")
  segments <- getSegments(sampleData)
  cghmcr <- cghMCR(segments, gapAllowed = 500, alteredLow = 0.20,
                   alteredHigh = 0.80, recurrence = 50)

I am a little confused , could you please help
thanks






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