Methfile_QC: Quality control for the input methylation file.

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Quality control for the input methylation file.

Description

This function discards the cytosine sites with low read coverage (quantile) or high read coverage (quantile).

Usage

Methfile_QC(
  inputmethfile,
  low_coveragenum = 10,
  high_coveragenum = NULL,
  low_quantile = NULL,
  high_quantile = 99.9,
  samplenum_QC = "all"
)

Arguments

inputmethfile	refers to the input of methylation file after Methfile_read().
low_coveragenum	refers to the minimum read coverage to be discarded, with default 10.
high_coveragenum	refers to the maximum read coverage to be discarded, with default NULL.
low_quantile	refers to the minimum quantile of read coverage to be discarded, with default NULL.
high_quantile	refers to the maximum quantile of read coverage to be discarded, with default 99.99.
samplenum_QC	refers to the sample numbers under quanlity control (e.g., samplenum_QC = 3 means that if three of five samples at one cytosine site have unqualified read coverage, then this site will be discarded), with default "all" samples.

Value

Outputs a data frame contain chromosome, position, and Cs & Ts for different replicates and groups after quality control.

Examples

inputmethfile_QC <- Methfile_QC(inputmethfile)
inputmethfile_QC <- Methfile_QC(inputmethfile, low_coveragenum = 20, high_quantile = 99.99)
inputmethfile_QC <- Methfile_QC(inputmethfile, low_coveragenum = 10, high_coveragenum = 100, samplenum_QC = 3)

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.