Man pages for xiaowangCN/GeneDMRs
GeneDMRs: an R package for Gene-based differentially methylated regions analysis
| Bedfile_read | Read the standard bedfile of refseq or cpgi downloaded from... |
| Boxplot_trans | Internal Use Function That transforms data for boxplot. |
| chromosmoe_sort | Internal Use Function That sorts the chromosomes from "chr1",... |
| Chromosome_pieplot | Pie plot based on different chromosomes. |
| Circos_plot | Plot the circos. |
| Correlation_plot | Plot the methylation correlation. |
| Cpgfeature_boxplot | Internal Use Function. That boxplots the methylation levels... |
| Cytofile_read | Read the cyto file. |
| DMC_feature | Annotate the differentially methylated cytosine (DMC) to... |
| DMC_methfile_QC | Merge the methylation file after quality control with DMCs |
| Enrich_plot | Enrich plot for GO terms and pathways. |
| Feature_pieplot | Pie plot based on different features. |
| Genebody_cpgfeature_boxplot | Boxplot the methylation levels for gene body based on CpG... |
| Group_boxplot | Boxplot the methylation levels for groups. |
| Group_cpgfeature_boxplot | Boxplot the methylation levels for groups based on CpG island... |
| Heatmap_plot | Heat map plot for chromosomes and features. |
| Logic_regression | Logistical regression analysis for each region or each... |
| Manhattan_plot | Manhattan plot for all cytosines or regions. |
| Meth_difference | Internal Use Function That calculates the methylation... |
| Methfile_QC | Quality control for the input methylation file. |
| Methfile_read | Read the methylation file. |
| Meth_mean | Internal Use Function That calculates the mean methylation... |
| Methmean_region | Calculate the methylation mean for regions. |
| Methmean_site | Calculate the methylation mean for cytosine sites. |
| Pvalue_adjusted | Internal Use Function That adjusts the P values of logistical... |
| Quick_DMCs | Quick use the GeneDMRs package for differentially methylated... |
| Quick_GeneDMRs | Quick use the GeneDMRs package for gene based differentially... |
| refseqfile_check | Internal Use Function That checks and annotates the promoter... |
| Regionfile_read | Internal Use Function That reads the bed file. |
| Sample_boxplot | Boxplot the methylation levels or read numbers in different... |
| Significant_filter | Filter the significant regions or cytosine sites. |
| Venn_plot | Venn plot for the common CpG island and CpG island shore. |
| Volcano_plot | Volcano plot for all the cytosines. |
| Window_divide | Divide the genome to windows. |
