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

This vignette gives an overview of the package GeneDMRs.

Overview

File read

---------------------------- ---------------------------------------------- Bedfile_read Read the standard bedfile of refseq or cpgi downloaded from UCSC Cytofile_read Read the cyto file Methfile_read Read the methylation file ---------------------------- ----------------------------------------------

Statistical analysis

---------------------------- ---------------------------------------------- Logic_regression Logistical regression analysis for each region or each cytosine site Methfile_QC Quality control for the input methylation file Methmean_region Calculate the methylation mean for regions Methmean_site Calculate the methylation mean for cytosine sites ---------------------------- ----------------------------------------------

Utility functions

---------------------------- ---------------------------------------------- DMC_feature Annotate the differentially methylated cytosine (DMC) to features DMC_methfile_QC Merge the methylation file after quality control with DMCs Significant_filter Filter the significant regions or cytosine sites Window_divide Divide the genome to windows ---------------------------- ----------------------------------------------

Graphics

---------------------------- ---------------------------------------------- Circos_plot Plot the circos Correlation_plot Plot the methylation correlation Chromosome_pieplot Pie plot based on different chromosomes Enrich_plot Enrich plot for GO terms and pathways Feature_pieplot Pie plot based on different features Group_boxplot Boxplot the methylation levels for groups Group_cpgfeature_boxplot Boxplot the methylation levels for groups based on CpG island features Genebody_cpgfeature_boxplot Boxplot the methylation levels for gene body based on CpG island features Heatmap_plot Heat map plot for chromosomes and features Manhattan_plot Manhattan plot for all cytosines or regions Sample_boxplot Boxplot the methylation levels or read numbers in different samples Venn_plot Venn plot for the common CpG island and CpG island shore Volcano_plot Volcano plot for all the cytosines ---------------------------- ----------------------------------------------

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