MethCP-class: Class 'MethCP'

In boyinggong/methcp: Differential methylation anlsysis for bisulfite sequencing data

Description

A class for performing DMR (differentially methylated region) detection analysis using method MethCP on whole genome bisulfite sequencing data.

The constructor function for MethCP objects.

Usage

MethCP(
  test = NA_character_,
  group1 = NA,
  group2 = NA,
  chr,
  pos,
  pvals,
  effect.size
)

MethCP(
    test = NA_character_, group1 = NA, group2 = NA, chr, pos,
    pvals, effect.size)

Arguments

test	a character string of the name of the per-cytosine statistcis.
group1	a character vector containing the sample names of the treatment group.
group2	a character vector containing the sample names of the control group.
chr	a character vector containing the cytosine chromosome infomation.
pos	a numeric vector containing the cytosine positions.
pvals	a numeric vector containing the p-values for each cytosine.
effect.size	a numeric vector containing the effect sizes for each cytosine.

Details

If not specified by function calcLociStatTimeCourse, calcLociStat, the parameter test can be set to any user-specified string indicating the name of the test performed.

In the cases where the goal is not to compare between treatment and control groups, parameter group1 and group2 can be set to NA.

If generated by calcLociStat, parameter stat will be a GRangesList object where each element in the list contains statistics for each of the chromosome in the dataset.

Value

A MethCP objects.

Slots

test

a character string of the name of the per-cytosine statistcis.

group1

a character vector containing the sample names of the treatment group.

group2

a character vector containing the sample names of the control group.

stat

a GRangesList object containing the results of per-cytosine tests.

segmentation

a GRanges object containing the segments and their infomation such as region-based statistics, coverages, etc.

Examples

obj <- MethCP(
    test = "myTest",
    group1 = paste0("Treatment", 1:3),
    group2 = paste0("Control", 1:3),
    chr = rep("Chr01", 5),
    pvals = c(0, 0.1, 0.9, NA, 0.02),
    pos = c(2, 5, 9, 10, 18),
    effect.size = c(1, -1, NA, 9, Inf))
# MethCP will omit the NAs and infinite values.
obj

boyinggong/methcp documentation built on April 25, 2021, 9 a.m.