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geneHapR (version 1.2.4)

Gene Haplotype Statistics, Phenotype Association and Visualization

Description

Import genome variants data and perform gene haplotype Statistics, visualization and phenotype association with 'R'.

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Version

Install

install.packages('geneHapR')

Monthly Downloads

499

Version

1.2.4

License

GPL-3

Maintainer

Zhang Renliang

Last Published

March 1st, 2024

Functions in geneHapR (1.2.4)

LDheatmap

This function produces a pairwise LD plot.
hapDistribution

Display of Geography Distribution
addPromoter

add promoter to annotation
ashaplotype

as.haplotype
displayVarOnGeneModel

Display Variants on Gene Model
filter_table

filter variants stored in table
filterLargeVCF

Pre-process of Large VCF File(s)
filter_vcf

Filter VCF
getGeneRanges

Get Gene Ranges
hapVsPheno

hapVsPheno
addINFO

Add Infomation to Haplotype Results
hapVsPhenos

hapVsPhenos
hap2hmp

Convert hapResult object to hapmap (hmp) format, for interact with other packages
siteEFF

Calculation of Sites Effective
hapVsPhenoPerSite

hapVsPhenoPerSite
hap_summary

Summary Hap Results
import_vcf

Import VCF from File
geneHapR-package

Gene Haplotype Statistics, Pheno Associations, and Visualization
network

Generate Haplotype Net Relationshop with Haplotype Result
getGenePOS

Get Gene Position
import_AccINFO

Import Accession Information from File
filter_hmp

filter variants in hapmap format
import_gff

Import Annotations from GFF Format File
import_hap

Import hapResult/hapSummary
filter_plink.pedmap

filter_plink.pedmap
import_MultipleAlignment

Import MultipleAlignment Result
plotHapTable2

plotHapTable2
sites_compar

sites comparison
plotHapNet

plotHapNet
plotHapTable

plotHapTable
import_plink.pedmap

import_plink.pedmap
import_seqs

Import Sequences
import_bed

import annotation files in BED format
table2hap

table2hap
vcf2hap

Generat Haps from VCF
plink.pedmap2hap

plink.pedmap2hap
seqs2hap

Generate Hap Results from Seqs
plotEFF

plotEFF
write.hap

Save Haplotype Results to Disk
SetATGas0

Set Position of ATG as Zero
filterLargep.link

Pre-process of Large VCF File(s)
filter_hap

Filter hap
DataSet

Datasets gff contains a example of gff file used for test of visualization mutations on gene model.