Description Usage Arguments Value
The BMIQ was developed by Andrew Teschendorff in 2013 and this implementation is the based on the version modified by Steve Horvath. I also removed and modified some parameters to simplify the function.
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beta.v |
A list of DNA methylation level |
design.v |
A list of probe design('I' or 'II') |
nfit |
number of probes of a given design type to use for the fitting. Default is 50000. Smaller values (~10000) will make BMIQ run faster at the expense of a small loss in accuracy. For most applications, 5000 or 10000 is ok. |
th1.v |
thresholds used for the initialisation of the EM-algorithm, they should represent buest guesses for calling probes hemi-methylated and methylated, and will be refined by the EM algorithm. Default values work well in most cases. |
niter |
maximum number of EM iterations to do. This number should be large enough to yield good fits to the type1 distribution. By default 5. |
tol |
tolerance convergence threshold for EM algorithm. By default 0.001. |
A data frame contains normalized m and um, p value, and DNA methylation level
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