geneHapR1.2.4 package

Add Infomation to Haplotype Results

add promoter to annotation

as.haplotype

Datasets gff contains a example of gff file used for test of visuali...

Display Variants on Gene Model

Filter hap

filter variants in hapmap format

filter_plink.pedmap

filter variants stored in table

Filter VCF

Pre-process of Large VCF File(s)

Pre-process of Large VCF File(s)

Gene Haplotype Statistics, Pheno Associations, and Visualization

Get Gene Position

Get Gene Ranges

Summary Hap Results

Convert hapResult object to hapmap (hmp) format, for interact with oth...

Display of Geography Distribution

hapVsPheno

hapVsPhenoPerSite

hapVsPhenos

Import Accession Information from File

import annotation files in BED format

Import Annotations from GFF Format File

Import hapResult/hapSummary

Import MultipleAlignment Result

import_plink.pedmap

Import Sequences

Import VCF from File

This function produces a pairwise LD plot.

Generate Haplotype Net Relationshop with Haplotype Result

plink.pedmap2hap

plotEFF

plotHapNet

plotHapTable

plotHapTable2

Generate Hap Results from Seqs

Set Position of ATG as Zero

Calculation of Sites Effective

sites comparison

table2hap

Generat Haps from VCF

Save Haplotype Results to Disk

the GUI interface of geneHapR