# Gene Haplotype Statistics, Phenotype Association and Visualization

## Documentation for package ‘geneHapR’ version 1.2.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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