DMR.analysis: Differential methylation analysis on pilot data

In liupeng2117/MethylSeqDesign: MethylSeqDesign: a power calucation and study design tool for Methyl-Seq

Differential methylation analysis on pilot data

Description

Differential methylation analysis on pilot data

Usage

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

Arguments

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.

Value

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.

liupeng2117/MethylSeqDesign documentation built on June 28, 2023, 7:09 a.m.