DMR.analysis: Differential methylation analysis on pilot data

Description Usage Arguments Value

Description

Differential methylation analysis on pilot data

Usage

1
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 May 29, 2019, 3:42 a.m.