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
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geneHapR_1.2.5.tgz(r-4.4-any)geneHapR_1.2.5.tgz(r-4.3-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:

nucleosomepositioning dataimport

45 exports 10 stars 1.79 score 160 dependencies 7 scripts 788 downloads

Last updated 12 days agofrom:1390bf269e. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 06 2024
R-4.5-win	WARNING	Sep 06 2024
R-4.5-linux	WARNING	Sep 06 2024
R-4.4-win	WARNING	Sep 06 2024
R-4.4-mac	WARNING	Sep 06 2024
R-4.3-win	WARNING	Aug 09 2024
R-4.3-mac	WARNING	Aug 09 2024

Exports:addINFO addPromoter as.haplotype displayVarOnGeneModel filter_hap filter_hmp filter_plink.pedmap filter_table filter_vcf filterLargeP.link filterLargeVCF get_hapNet getGenePOS getGeneRanges getHapGroup gffSetATGas0 hap_summary hap2hmp hapDistribution hapSetATGas0 hapVsPheno hapVsPhenoPerSite hapVsPhenos hmp2hap import_AccINFO import_bed import_gff import_hap import_MultipleAlignment import_plink.pedmap import_seqs import_vcf plink.pedmap2hap plot_LDheatmap plotEFF plotHapNet plotHapTable plotHapTable2 seqs2hap siteEFF sites table2hap trimSeqs vcf2hap write.hap

Dependencies:abind ape askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops boot broom bslib cachem car carData class classInt cli cluster codetools colorspace combinat commonmark corrplot cowplot cpp11 crayon curl DBI DelayedArray Deriv digest doBy dplyr e1071 fansi farver fastmap fontawesome formatR fs futile.logger futile.options gdata generics genetics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra grImport gtable gtools htmltools httpuv httr IRanges isoband jquerylib jsonlite KernSmooth labeling lambda.r later lattice lifecycle lme4 lolliplot magrittr maps MASS Matrix MatrixGenerics MatrixModels matrixStats memoise memuse mgcv microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pegas permute pillar pinfsc50 pkgconfig plyr polynom promises proxy purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools rstatix rtracklayer s2 S4Arrays S4Vectors sass scales sf shiny shinyjs snow sourcetools SparseArray SparseM stringdist stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils units utf8 vcfR vctrs vegan viridisLite withr wk XML xtable XVector yaml zlibbioc

Introduction of 'geneHapR'

Rendered fromIntroduction_of_geneHapR.Rmdusingknitr::rmarkdownon Sep 06 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add Infomation to Haplotype Results	addINFO sites
add promoter to annotation	addPromoter
as.haplotype	as.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 Model	displayVarOnGeneModel
Filter hap	filter_hap
filter variants in hapmap format	filter_hmp
filter_plink.pedmap	filter_plink.pedmap
filter variants stored in table	filter_table
Filter VCF	filter_vcf
Pre-process of Large VCF File(s)	filterLargeP.link filterLargep.link
Pre-process of Large VCF File(s)	filterLargeVCF
Get Gene Position	getGenePOS
Get Gene Ranges	getGeneRanges
Summary Hap Results	hap_summary
Convert hapResult object to hapmap (hmp) format, for interact with other packages	hap2hmp hmp2hap
Display of Geography Distribution	hapDistribution
hapVsPheno	hapVsPheno
hapVsPhenoPerSite	hapVsPhenoPerSite
hapVsPhenos	hapVsPhenos
Import Accession Information from File	import_AccINFO
import annotation files in BED format	import_bed
Import Annotations from GFF Format File	import_gff
Import hapResult/hapSummary	import_hap
Import MultipleAlignment Result	import_MultipleAlignment
import_plink.pedmap	import_plink.pedmap
Import Sequences	import_seqs
Import VCF from File	import_vcf
This function produces a pairwise LD plot.	LDheatmap plot_LDheatmap
Generate Haplotype Net Relationshop with Haplotype Result	getHapGroup get_hapNet network
plink.pedmap2hap	plink.pedmap2hap
plotEFF	plotEFF
plotHapNet	plotHapNet
plotHapTable	plotHapTable
plotHapTable2	plotHapTable2
Generate Hap Results from Seqs	seqs2hap trimSeqs
Set Position of ATG as Zero	gffSetATGas0 hapSetATGas0 SetATGas0
Calculation of Sites Effective	siteEFF
sites comparison	compareAllSites sites_compar
table2hap	table2hap
Generat Haps from VCF	vcf2hap
Save Haplotype Results to Disk	write.hap