Package: isoRelate 0.1.0

Lyndal Henden

isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Pairwise identity by descent inference of haploid species using single nucleotide polymorphism data. isoRelate can detect IBD in the presence of multi-clonal infections and also provides a function for identifying loci under recent positive selection.

Authors:Lyndal Henden [aut, cre]

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isoRelate.pdf |isoRelate.html✨
isoRelate/json (API)

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

Peer review:

Bug tracker:https://github.com/bahlolab/isorelate/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • annotation_genes - Plasmodium Falciparum Gene Annotation Dataset
  • highlight_genes - Plasmodium Falciparum Gene Highlight Dataset
  • my_ibd - IBD Segments For The Papua New Guinea Dataset
  • png_genotypes - Filtered Genotypes For The Papua New Guinea Dataset
  • png_ibd - IBD Segments For The Papua New Guinea Dataset
  • png_parameters - IBD Parameter Estimates For The Papua New Guinea Dataset
  • png_pedmap - Papua New Guinea Plasmodium Falciparum Dataset

On CRAN:

performs

2.48 score 6 stars 7 scripts 19 exports 43 dependencies

Last updated 7 years agofrom:109ee470f1. Checks:ERROR: 9. Indexed: no.

TargetResultDate
Doc / VignettesFAILOct 25 2024
R-4.5-win-x86_64ERROROct 25 2024
R-4.5-linux-x86_64ERROROct 25 2024
R-4.4-win-x86_64ERROROct 25 2024
R-4.4-mac-x86_64ERROROct 25 2024
R-4.4-mac-aarch64ERROROct 25 2024
R-4.3-win-x86_64ERROROct 25 2024
R-4.3-mac-x86_64ERROROct 25 2024
R-4.3-mac-aarch64ERROROct 25 2024

Exports:calculateMissingnesscalculatePopAlleleFreqgetGenotypesgetIBDiclustersgetIBDiRgetIBDmatrixgetIBDparametersgetIBDpclustersgetIBDposteriorgetIBDproportiongetIBDsegmentsgetIBDsummarygroupPairsIBDMatrixisolatePairsplotIBDclustersplotIBDiRplotIBDproportionsplotIBDsegments

Dependencies:clicodacodetoolscolorspacecpp11data.tabledoParallelfansifarverforeachggnetworkggplot2ggrepelgluegtableigraphintergraphisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnetworknlmepillarpkgconfigR6RColorBrewerRcpprlangscalessnastatnet.commontibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
The matrix A in the equation Ax=b for 2 diploid chromosomesAmatrixDD
The matrix A in the equation Ax=b for 1 haploid and 1 diploid chromosomeAmatrixHD
The matrix A in the equation Ax=b for 2 haploid chromosomesAmatrixHH
Plasmodium Falciparum Gene Annotation Datasetannotation_genes
Internal functionareColors
The vector b in the equation Ax=b for 2 diploid chromosomesbVectorDD
The vector b in the equation Ax=b for 1 haploid chromosome and 1 diploid chromosomebVectorHD
The vector b in the equation Ax=b for 2 haploid chromosomesbVectorHH
Calculate alphacalculateAlpha
Calculate betacalculateBeta
Calculate gammacalculateGamma
Calculate the log-likelihood of the datacalculateLogLikelihood
Estimation of MeiosiscalculateMeiosis
Calculate Missingness ProportionscalculateMissingness
Calculate Allele Frequencies for SNPs from Genotype DatacalculatePopAlleleFreq
Calculate scalecalculateScale
Calculate the Viterbi sequencecalculateViterbi
A function that prints summary information of clustersclusterSummary
The emission probabilities for 2 diploid chromosomesemissionProbDD
The emission probabilities for 1 haploid chromosome and 1 diploid chromosomeemissionProbHD
The emission probabilities for 2 haploid chromosomesemissionProbHH
Calculating the emission probability sumation when missing genotype calls presentemissionProbMissingGeno
The genotyping error probability for 1 diploid chromosomegenotypeErrorD
The genotyping error probability for 1 haploid chromosomegenotypeErrorH
IsoRelate Colour Palette for groupsgetColourPaletteMajor
'getColourPaletteMinor()' generates a specified number of shades of a given colour.getColourPaletteMinor
Pre-Analysis Data ProcessinggetGenotypes
Interval Cluster NetworksgetIBDiclusters
Selection Significance StatisticgetIBDiR
Binary IBD MatrixgetIBDmatrix
Parameter EstimationgetIBDparameters
Genome Cluster NetworksgetIBDpclusters
IBD Posterior ProbabilitiesgetIBDposterior
Proportion of Pairs IBDgetIBDproportion
IBD Segment DetectiongetIBDsegments
IBD Segment SummarygetIBDsummary
function to find IBD that overlap intervalgetOverlap
Group Combinations for AnalysisgroupPairs
Call Genotypes from Haplotype DatahaplotypeToGenotype
Plasmodium Falciparum Gene Highlight Datasethighlight_genes
Internal FunctionIBDLabel
Binary Matrix of IBDIBDMatrix
IBDparameters() calculates IBD probabilities then estimates the number of meiosis for an isolate pair.IBDparameters
Internal FunctionIBDTable
Internal FunctioniRfunction
Pair Combinations for AnalysisisolatePairs
Internal Functionmerge_lists
IBD Segments For The Papua New Guinea Datasetmy_ibd
Plot Cluster NetworksplotIBDclusters
Plot iR StatisticsplotIBDiR
Plot The Proportion of Pairs IBDplotIBDproportions
Plot IBD SegmentsplotIBDsegments
Filtered Genotypes For The Papua New Guinea Datasetpng_genotypes
IBD Segments For The Papua New Guinea Datasetpng_ibd
IBD Parameter Estimates For The Papua New Guinea Datasetpng_parameters
Papua New Guinea Plasmodium Falciparum Datasetpng_pedmap
Round digits to specified decimal placesroundDecimal
The transition probabilities for 2 diploid chromosomestransitionProbDD
The transition probabilities for 1 haploid and 1 diploid chromosometransitionProbHD
The transition probabilities for 2 haploid chromosomestransitionProbHH
Matrices of all possible genotype combinations between pairs, given MOItrueGenotypes