Package: paneljudge 0.0.0.9000
Aimee Taylor
paneljudge: Judge the performance of a panel of genetic markers using simulated data
An R package to judge the performance of a panel of genetic markers using data simulated for pairs of haploid genotypes. The data are simulated under a hidden Markov model of relatedness (described in Taylor, A.R., Jacob, P.E., Neafsey, D.E. and Buckee, C.O., 2019. Estimating relatedness between malaria parasites. Genetics, 212(4), pp.1337-1351) using allele frequency estimates provided by the user and inter-marker distances. The markers are treated as categorical random variables whose realisations (alleles) are unordered. The effective cardinalities and diversities of the markers can be computed using the input allele frequency estimates. Panel performance can be judged in terms of the root mean square error (RMSE) and confidence interval width of estimated relatedness, where relatedness is estimated under the same model used to simulate the data. At present, the examples we provide do not consider model misspecification; do not account for uncertainty around input allele frequency estimates; do not consider relatedness between pairs of haploid genotypes simulated using different allele frequencies; do not account for marker drop-out (markers that fail to produce useful data, e.g. because they a monomorphic). Otherwise stated, in the examples provided, the performance of a panel is judged in its most favourable light; it will likely perform less well in reality.
Authors:
paneljudge_0.0.0.9000.tar.gz
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paneljudge.pdf |paneljudge.html✨
paneljudge/json (API)
| # Install paneljudge in R: |
| install.packages('paneljudge', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aimeertaylor/paneljudge/issues
- chr_lengths - Data on chromosome lengths.
- frequencies - Data on allele frequencies of the example GTseq panel.
- markers - Data on markers of the example GTseq panel.
Last updated 1 years agofrom:b489f6ab4669d0d3c6ff6e3bdfa9666375889a31
Exports:compute_diversitiescompute_eff_cardinalitiescompute_r_and_k_CIsestimate_r_and_ksimulate_Ys
Dependencies:codetoolsdigestdoParalleldoRNGforeachiteratorsRcpprngtools
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data on chromosome lengths. | chr_lengths |
| Function to compute marker diversities | compute_diversities |
| Function to compute marker effective cardinalities | compute_eff_cardinalities |
| Function to compute confidence intervals for relatedness and switch rate parameters | compute_r_and_k_CIs |
| Function to estimate relatedness and switch rate parameters | estimate_r_and_k |
| Data on allele frequencies of the example GTseq panel. | frequencies |
| Data on markers of the example GTseq panel. | markers |
| Function to simulate genotype calls for a pair of haploid genotypes | simulate_Ys |
