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call_cnvr()
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Generate CNV Regions (CNVR) |
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call_gene()
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Annotate gene for intervals (CNV, CNVR, ROH or QTL) |
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clean_ensgene()
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Clean Ensembl reference gene list |
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clean_ucsc()
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Clean USCS reference gene list |
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closer_snp()
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Pick out the names and positions of start and end SNPs of a genomic interval |
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cnvr_plot()
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Custom CNVR distribution map and plot all high frequency CNVR at once |
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cnv_clean()
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Clean CNV |
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cnv_summary_plot()
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Summary plots for CNVs |
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cnv_visual()
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Custom visualizing CNV |
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compare_cnv()
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Compare CNV |
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compare_cnvr()
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Compare CNVR |
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compare_gene()
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Find the consensus genes by comparing the frequency of gene in which has CNV status |
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compare_interval()
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Title compare_interval
compare cnvr, each input file should contain Chr, Start and End columns,
the Chr column should be the number only, for example: 1 not chr1 |
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convert_coord()
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Convert coordinates of genomic intervals |
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convert_map()
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Convert map file |
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get_demo()
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Get demo data |
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get_haplotype()
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Get haplotype |
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get_refgene()
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Get reference gene |
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get_samples()
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Title get_samples |
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haplo_visual()
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The order of haplotype present in plot are start from high frequency to low from top to bottom |
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plot_cnvr_panorama()
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Plotting CNVR with all relevant information |
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plot_cnvr_source()
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Plotting CNVs by the source information |
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plot_gene()
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Custom plotting gene from reference gene list |
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plot_snp_density()
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Title SNP density plot |
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prep_phased()
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Prepare the phased genotype into the standard format |
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roh_visual()
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Custom Visualizing ROH |
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roh_window()
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Sliding window to capture the high frequent ROH region |