Gene Haplotype Statistics, Phenotype Association and
Visualization
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Documentation for package ‘geneHapR’ version 1.2.4
Help Pages
| AccINFO | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| addINFO | Add Infomation to Haplotype Results |
| addPromoter | add promoter to annotation |
| as.haplotype | as.haplotype |
| ashaplotype | as.haplotype |
| china | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| compareAllSites | sites comparison |
| DataSet | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| displayVarOnGeneModel | Display Variants on Gene Model |
| filterLargeP.link | Pre-process of Large VCF File(s) |
| filterLargep.link | Pre-process of Large VCF File(s) |
| filterLargeVCF | Pre-process of Large VCF File(s) |
| filter_hap | Filter hap |
| filter_hmp | filter variants in hapmap format |
| filter_plink.pedmap | filter_plink.pedmap |
| filter_table | filter variants stored in table |
| filter_vcf | Filter VCF |
| getGenePOS | Get Gene Position |
| getGeneRanges | Get Gene Ranges |
| getHapGroup | Generate Haplotype Net Relationshop with Haplotype Result |
| get_hapNet | Generate Haplotype Net Relationshop with Haplotype Result |
| gff | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| gffSetATGas0 | Set Position of ATG as Zero |
| gt.geno | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| hap2hmp | Convert hapResult object to hapmap (hmp) format, for interact with other packages |
| hapDistribution | Display of Geography Distribution |
| hapResult | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| hapSetATGas0 | Set Position of ATG as Zero |
| hapVsPheno | hapVsPheno |
| hapVsPhenoPerSite | hapVsPhenoPerSite |
| hapVsPhenos | hapVsPhenos |
| hap_summary | Summary Hap Results |
| hmp2hap | Convert hapResult object to hapmap (hmp) format, for interact with other packages |
| import_AccINFO | Import Accession Information from File |
| import_bed | import annotation files in BED format |
| import_gff | Import Annotations from GFF Format File |
| import_hap | Import hapResult/hapSummary |
| import_MultipleAlignment | Import MultipleAlignment Result |
| import_plink.pedmap | import_plink.pedmap |
| import_seqs | Import Sequences |
| import_vcf | Import VCF from File |
| LDheatmap | This function produces a pairwise LD plot. |
| network | Generate Haplotype Net Relationshop with Haplotype Result |
| pheno | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| plink.pedmap2hap | plink.pedmap2hap |
| plotEFF | plotEFF |
| plotHapNet | plotHapNet |
| plotHapTable | plotHapTable |
| plotHapTable2 | plotHapTable2 |
| plot_LDheatmap | This function produces a pairwise LD plot. |
| seqs | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| seqs2hap | Generate Hap Results from Seqs |
| SetATGas0 | Set Position of ATG as Zero |
| siteEFF | Calculation of Sites Effective |
| sites | Add Infomation to Haplotype Results |
| sites_compar | sites comparison |
| table2hap | table2hap |
| trimSeqs | Generate Hap Results from Seqs |
| vcf | Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
| vcf2hap | Generat Haps from VCF |
| write.hap | Save Haplotype Results to Disk |