Man pages for JH-Zhou/HandyCNV
HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH
| call_cnvr | Generate CNV Regions (CNVR) |
| call_gene | Annotate gene for intervals (CNV, CNVR, ROH or QTL) |
| clean_ensgene | Clean Ensembl reference gene list |
| clean_ucsc | Clean USCS reference gene list |
| closer_snp | Pick out the names and positions of start and end SNPs of a... |
| cnv_clean | Clean CNV |
| cnvr_plot | Custom CNVR distribution map and plot all high frequency CNVR... |
| cnv_summary_plot | Summary plots for CNVs |
| cnv_visual | Custom visualizing CNV |
| compare_cnv | Compare CNV |
| compare_cnvr | Compare CNVR |
| compare_gene | Find the consensus genes by comparing the frequency of gene... |
| compare_interval | Title compare_interval compare cnvr, each input file should... |
| convert_coord | Convert coordinates of genomic intervals |
| convert_map | Convert map file |
| get_demo | Get demo data |
| get_haplotype | Get haplotype |
| get_refgene | Get reference gene |
| get_samples | Title get_samples |
| haplo_visual | The order of haplotype present in plot are start from high... |
| plot_cnvr_panorama | Plotting CNVR with all relevant information |
| plot_cnvr_source | Plotting CNVs by the source information |
| plot_gene | Custom plotting gene from reference gene list |
| plot_snp_density | Title SNP density plot |
| prep_phased | Prepare the phased genotype into the standard format |
| roh_visual | Custom Visualizing ROH |
| roh_window | Sliding window to capture the high frequent ROH region |
