Package: genetics 1.3.8.1.3
genetics: Population Genetics
Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
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genetics.pdf |genetics.html✨
genetics/json (API)
NEWS
| # Install 'genetics' in R: |
| install.packages('genetics', repos = c('https://warnes.r-universe.dev', 'https://cloud.r-project.org')) |
- gregorius - Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:b96215a2ce. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | NOTE | Sep 13 2024 |
| R-4.5-linux | NOTE | Sep 13 2024 |
| R-4.4-win | NOTE | Sep 13 2024 |
| R-4.4-mac | NOTE | Sep 13 2024 |
| R-4.3-win | NOTE | Sep 13 2024 |
| R-4.3-mac | NOTE | Sep 13 2024 |
Exports:%in%alleleallele.countallele.namesas.factoras.genotypeas.genotype.allele.countas.haplotypecarrierci.balancediseqdiseq.ciexpectedGenotypesexpectedHaplotypesgenegene<-geno.as.arraygenotypegenotypeOrdergenotypeOrder<-getgenegetlocusgetmarkergregoriusgroupGenotypehaphapambighapenumhapfreqhaplotypehapmcmchapshuffleheterozygotehomozygoteHWE.chisqHWE.exactHWE.testis.geneis.genotypeis.haplotypeis.locusis.markerLDLDplotLDtablelocuslocus<-makeGenotypesmakeHaplotypesmarkermarker<-mourantnalleleorderpower.casectrlshortsummary.genotypesummary.LD.data.framewrite.marker.filewrite.pedigree.filewrite.pop.file
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding' the Interval on the Quantile Scale. | ci.balance |
| Depreciated functions | power.casectrl |
| Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium | diseq diseq.ci diseq.genotype diseq.table print.diseq |
| Construct expected genotypes/haplotypes according to known allele variants | expectedGenotypes expectedHaplotypes |
| Genotype or Haplotype Objects. | %in% %in%.default %in%.genotype %in%.haplotype ==.genotype ==.haplotype allele.count.genotype as.genotype as.genotype.allele.count as.genotype.character as.genotype.default as.genotype.factor as.genotype.genotype as.genotype.haplotype as.genotype.table as.haplotype genotype haplotype heterozygote.genotype homozygote.genotype is.genotype is.haplotype nallele print.allele.count print.allele.genotype print.genotype [.genotype [.haplotype [<-.genotype [<-.haplotype |
| Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size. | gregorius |
| Group genotype values | groupGenotype |
| Extract Features of Genotype objects | allele allele.count allele.names carrier carrier.genotype heterozygote homozygote |
| Perform Chi-Square Test for Hardy-Weinberg Equilibrium | HWE.chisq HWE.chisq.genotype |
| Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers | HWE.exact |
| Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium | HWE.test HWE.test.data.frame HWE.test.genotype print.HWE.test |
| Pairwise linkage disequilibrium between genetic markers. | LD LD.data.frame LD.genotype |
| Create and Manipulate Locus, Gene, and Marker Objects | as.character.gene as.character.locus as.character.marker gene gene<- getgene getlocus getmarker is.gene is.locus is.marker locus locus<- marker marker<- print.gene print.locus print.marker |
| Convert columns in a dataframe to genotypes or haplotypes | makeGenotypes makeHaplotypes |
| Order/sort genotype/haplotype object | genotypeOrder genotypeOrder<- order order.genotype sort.genotype |
| Plot genotype object | plot.genotype |
| Textual and graphical display of linkage disequilibrium (LD) objects | LDplot LDtable plot.LD.data.frame print.LD print.LD.data.frame print.summary.LD.data.frame summary.LD.data.frame |
| Allele and Genotype Frequency from a Genotype or Haplotype Object | print.summary.genotype summary.genotype |
| Undocumented functions | allele.count.2.genotype as.factor as.factor.allele.genotype as.factor.default as.factor.genotype geno.as.array hap hapambig hapenum hapfreq hapmcmc hapshuffle mknum mourant shortsummary.genotype |
| Create genetics data files | write.marker.file write.pedigree.file write.pop.file |
