Package: geneHapR 1.2.5

geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

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

Authors:Zhang Renliang [aut, cre], Jia Guanqing [aut]

geneHapR_1.2.5.tar.gz
geneHapR_1.2.5.zip(r-4.5)geneHapR_1.2.5.zip(r-4.4)geneHapR_1.2.5.zip(r-4.3)
geneHapR_1.2.5.tgz(r-4.5-any)geneHapR_1.2.5.tgz(r-4.4-any)
geneHapR_1.2.5.tar.gz(r-4.5-noble)geneHapR_1.2.5.tar.gz(r-4.4-noble)
geneHapR_1.2.5.tgz(r-4.4-emscripten)geneHapR_1.2.5.tgz(r-4.3-emscripten)
geneHapR.pdf |geneHapR.html✨
geneHapR/json (API)

# Install 'geneHapR' in R:
install.packages('geneHapR', repos = c('https://zhangrenl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhangrenl/genehapr/issues

Datasets:
  • AccINFO - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • china - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • gff - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • gt.geno - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • hapResult - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • pheno - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • seqs - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.
  • vcf - Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.

On CRAN:

Conda:

nucleosomepositioningdataimport

5.11 score 13 stars 8 scripts 700 downloads 45 exports 163 dependencies

Last updated 6 months agofrom:1390bf269e. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 05 2025
R-4.5-winWARNINGMar 05 2025
R-4.5-macWARNINGMar 05 2025
R-4.5-linuxWARNINGMar 05 2025
R-4.4-winWARNINGMar 05 2025
R-4.4-macWARNINGMar 05 2025
R-4.4-linuxWARNINGMar 05 2025
R-4.3-winWARNINGMar 05 2025

Exports:addINFOaddPromoteras.haplotypedisplayVarOnGeneModelfilter_hapfilter_hmpfilter_plink.pedmapfilter_tablefilter_vcffilterLargeP.linkfilterLargeVCFget_hapNetgetGenePOSgetGeneRangesgetHapGroupgffSetATGas0hap_summaryhap2hmphapDistributionhapSetATGas0hapVsPhenohapVsPhenoPerSitehapVsPhenoshmp2hapimport_AccINFOimport_bedimport_gffimport_hapimport_MultipleAlignmentimport_plink.pedmapimport_seqsimport_vcfplink.pedmap2happlot_LDheatmapplotEFFplotHapNetplotHapTableplotHapTable2seqs2hapsiteEFFsitestable2haptrimSeqsvcf2hapwrite.hap

Dependencies:abindapeaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroombslibcachemcarcarDataclassclassIntcliclustercodetoolscolorspacecombinatcommonmarkcorrplotcowplotcpp11crayoncurlDBIDelayedArrayDerivdigestdoBydplyre1071fansifarverfastmapfontawesomeformatRFormulafsfutile.loggerfutile.optionsgdatagenericsgeneticsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragrImportgtablegtoolshtmltoolshttpuvhttrIRangesisobandjquerylibjsonliteKernSmoothlabelinglambda.rlaterlatticelifecyclelme4lolliplotmagrittrmapsMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisememusemgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpegaspermutepillarpinfsc50pkgconfigplyrpolynompromisesproxypurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasreshape2restfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayers2S4ArraysS4VectorssassscalessfshinyshinyjssnowsourcetoolsSparseArraySparseMstringdiststringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsunitsutf8vcfRvctrsveganviridisLitewithrwkXMLxtableXVectoryaml

Introduction of 'geneHapR'

Rendered fromIntroduction_of_geneHapR.Rmdusingknitr::rmarkdownon Mar 05 2025.

Last update: 2023-03-07
Started: 2022-07-13

Readme and manuals

Help Manual

Help pageTopics
Add Infomation to Haplotype ResultsaddINFO sites
add promoter to annotationaddPromoter
as.haplotypeas.haplotype ashaplotype
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model.AccINFO china DataSet gff gt.geno hapResult pheno seqs vcf
Display Variants on Gene ModeldisplayVarOnGeneModel
Filter hapfilter_hap
filter variants in hapmap formatfilter_hmp
filter_plink.pedmapfilter_plink.pedmap
filter variants stored in tablefilter_table
Filter VCFfilter_vcf
Pre-process of Large VCF File(s)filterLargeP.link filterLargep.link
Pre-process of Large VCF File(s)filterLargeVCF
Get Gene PositiongetGenePOS
Get Gene RangesgetGeneRanges
Summary Hap Resultshap_summary
Convert hapResult object to hapmap (hmp) format, for interact with other packageshap2hmp hmp2hap
Display of Geography DistributionhapDistribution
hapVsPhenohapVsPheno
hapVsPhenoPerSitehapVsPhenoPerSite
hapVsPhenoshapVsPhenos
Import Accession Information from Fileimport_AccINFO
import annotation files in BED formatimport_bed
Import Annotations from GFF Format Fileimport_gff
Import hapResult/hapSummaryimport_hap
Import MultipleAlignment Resultimport_MultipleAlignment
import_plink.pedmapimport_plink.pedmap
Import Sequencesimport_seqs
Import VCF from Fileimport_vcf
This function produces a pairwise LD plot.LDheatmap plot_LDheatmap
Generate Haplotype Net Relationshop with Haplotype ResultgetHapGroup get_hapNet network
plink.pedmap2happlink.pedmap2hap
plotEFFplotEFF
plotHapNetplotHapNet
plotHapTableplotHapTable
plotHapTable2plotHapTable2
Generate Hap Results from Seqsseqs2hap trimSeqs
Set Position of ATG as ZerogffSetATGas0 hapSetATGas0 SetATGas0
Calculation of Sites EffectivesiteEFF
sites comparisoncompareAllSites sites_compar
table2haptable2hap
Generat Haps from VCFvcf2hap
Save Haplotype Results to Diskwrite.hap