Help on cghMCR units of gapAllowed
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nac ▴ 280
@nac-4545
Last seen 7.1 years ago
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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
DNAcopy cghMCR DNAcopy cghMCR • 628 views
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