Dinh/Dinh 2012/NOTES/2012-2-10

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Tech Rep 9[edit]

  • SimulationResults_2082012 finished running
  • Initial analysis using R:
> A = read.table("SimulationResults_2082012", header=FALSE)
> cor(abs(A$V13-0.5), A$V14/200)
NOTE: column V13 is the estimated mean methylation fraction
NOTE: column V14 is the sum of the simulated standard deviation (there are 200 of them)
correlation of mean methylation fraction and standard deviation is : Pearson's r = -0.703 (the farther from 0.5, the lower the standard deviation)

Bisulfite Patch PCR[edit]

  • Current status of the program:
    • Objectives:
 1) enzyme(s) that can make the best pieces (scored by #of target CpGs)
    • Procedure:
 0) Set of enzyme(s)
 1) Take all possible cut-sites wSNP and woSNP
 2) Obtain "usable" pieces from cut-sites(woSNP)
    "usable" pieces are: 100-200bp and contain >=1 target CpGs and does not contain cut-sites(wSNP)
    Note that "unusable" pieces may contain cut-sites(wSNP). And all pieces considered are by cut-sites(woSNP)
 4) Count only #of target CpGs which are in "usable" pieces
 5) Keep enzyme(s) set which gives the highest #of target CpGs
  • Finer details:
 We obtain cut-sites(wSNP) by enumerating possible every word(of lengths 3-29) in the target region with up to 3 SNPs.
  • Michelle incorporated the code to build cut-sites(wSNP).