Description Usage Arguments Value

Differential methylation analysis on pilot data

1 | ```
DMR.analysis(N0, cov.matrix, methyl.matrix, R, pilot.R)
``` |

`N0` |
the sample size of the pilot data per group. If the two groups of the pilot data have different sample size, input can be a vector of length 2 specifying the sample size for each group. |

`cov.matrix` |
a numeric matrix or data frame of coverage, the rows are genes and columns are samples. |

`methyl.matrix` |
a numeric matrix or data frame of methylated read count, the rows are genes and columns are samples. A one to one correspondence between the matrix of methylated read count and the matrix of coverage is required. |

`R` |
the targeted sequencing depth in number of lanes. Input can be a vector. R is no larger than pilot.R. |

`piot.R` |
Sequencing depth of pilot data in number of lanes. |

a list of three element, the first element is the p values from DM analysis, the second element is a matrix of GLM model parameters and estimated tagwise dispersion for each region. The third element is a matrix of ratios for different sequencing depth.

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