dot-BMIQ: Beta MIxture Quantile dilation (BMIQ)

Description Usage Arguments Value

Description

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.

Usage

1
2
.BMIQ(beta.v, design.v, nfit = 50000, th1.v = c(0.2, 0.75),
  niter = 5, tol = 0.001)

Arguments

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.

Value

A data frame contains normalized m and um, p value, and DNA methylation level


MengweiLi-project/gmqn documentation built on Feb. 26, 2020, 11:35 a.m.