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'))

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

19 exports 6 stars 0.71 score 43 dependencies

Last updated 6 years agofrom:109ee470f1d1e9e4cd131045c23eea7047cff649

Exports:calculateMissingness calculatePopAlleleFreq getGenotypes getIBDiclusters getIBDiR getIBDmatrix getIBDparameters getIBDpclusters getIBDposterior getIBDproportion getIBDsegments getIBDsummary groupPairs IBDMatrix isolatePairs plotIBDclusters plotIBDiR plotIBDproportions plotIBDsegments

Dependencies:cli coda codetools colorspace cpp11 data.table doParallel fansi farver foreach ggnetwork ggplot2 ggrepel glue gtable igraph intergraph isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell network nlme pillar pkgconfig R6 RColorBrewer Rcpp rlang scales sna statnet.common tibble utf8 vctrs viridisLite withr

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The matrix A in the equation Ax=b for 2 diploid chromosomes	AmatrixDD
The matrix A in the equation Ax=b for 1 haploid and 1 diploid chromosome	AmatrixHD
The matrix A in the equation Ax=b for 2 haploid chromosomes	AmatrixHH
Plasmodium Falciparum Gene Annotation Dataset	annotation_genes
Internal function	areColors
The vector b in the equation Ax=b for 2 diploid chromosomes	bVectorDD
The vector b in the equation Ax=b for 1 haploid chromosome and 1 diploid chromosome	bVectorHD
The vector b in the equation Ax=b for 2 haploid chromosomes	bVectorHH
Calculate alpha	calculateAlpha
Calculate beta	calculateBeta
Calculate gamma	calculateGamma
Calculate the log-likelihood of the data	calculateLogLikelihood
Estimation of Meiosis	calculateMeiosis
Calculate Missingness Proportions	calculateMissingness
Calculate Allele Frequencies for SNPs from Genotype Data	calculatePopAlleleFreq
Calculate scale	calculateScale
Calculate the Viterbi sequence	calculateViterbi
A function that prints summary information of clusters	clusterSummary
The emission probabilities for 2 diploid chromosomes	emissionProbDD
The emission probabilities for 1 haploid chromosome and 1 diploid chromosome	emissionProbHD
The emission probabilities for 2 haploid chromosomes	emissionProbHH
Calculating the emission probability sumation when missing genotype calls present	emissionProbMissingGeno
The genotyping error probability for 1 diploid chromosome	genotypeErrorD
The genotyping error probability for 1 haploid chromosome	genotypeErrorH
IsoRelate Colour Palette for groups	getColourPaletteMajor
'getColourPaletteMinor()' generates a specified number of shades of a given colour.	getColourPaletteMinor
Pre-Analysis Data Processing	getGenotypes
Interval Cluster Networks	getIBDiclusters
Selection Significance Statistic	getIBDiR
Binary IBD Matrix	getIBDmatrix
Parameter Estimation	getIBDparameters
Genome Cluster Networks	getIBDpclusters
IBD Posterior Probabilities	getIBDposterior
Proportion of Pairs IBD	getIBDproportion
IBD Segment Detection	getIBDsegments
IBD Segment Summary	getIBDsummary
function to find IBD that overlap interval	getOverlap
Group Combinations for Analysis	groupPairs
Call Genotypes from Haplotype Data	haplotypeToGenotype
Plasmodium Falciparum Gene Highlight Dataset	highlight_genes
Internal Function	IBDLabel
Binary Matrix of IBD	IBDMatrix
IBDparameters() calculates IBD probabilities then estimates the number of meiosis for an isolate pair.	IBDparameters
Internal Function	IBDTable
Internal Function	iRfunction
Pair Combinations for Analysis	isolatePairs
Internal Function	merge_lists
IBD Segments For The Papua New Guinea Dataset	my_ibd
Plot Cluster Networks	plotIBDclusters
Plot iR Statistics	plotIBDiR
Plot The Proportion of Pairs IBD	plotIBDproportions
Plot IBD Segments	plotIBDsegments
Filtered Genotypes For The Papua New Guinea Dataset	png_genotypes
IBD Segments For The Papua New Guinea Dataset	png_ibd
IBD Parameter Estimates For The Papua New Guinea Dataset	png_parameters
Papua New Guinea Plasmodium Falciparum Dataset	png_pedmap
Round digits to specified decimal places	roundDecimal
The transition probabilities for 2 diploid chromosomes	transitionProbDD
The transition probabilities for 1 haploid and 1 diploid chromosome	transitionProbHD
The transition probabilities for 2 haploid chromosomes	transitionProbHH
Matrices of all possible genotype combinations between pairs, given MOI	trueGenotypes