Package: MIPanalyzer 1.1.0

Bob Verity

MIPanalyzer: Filtering and analysis of MIP data

Filtering and analysis of MIP data.

Authors:Bob Verity [aut, cre]

MIPanalyzer_1.1.0.tar.gz
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MIPanalyzer_1.1.0.tgz(r-4.4-x86_64)MIPanalyzer_1.1.0.tgz(r-4.4-arm64)MIPanalyzer_1.1.0.tgz(r-4.3-x86_64)MIPanalyzer_1.1.0.tgz(r-4.3-arm64)
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MIPanalyzer.pdf |MIPanalyzer.html✨
MIPanalyzer/json (API)

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

Peer review:

Bug tracker:https://github.com/mrc-ide/mipanalyzer/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

4.17 score 2 stars 37 scripts 38 exports 88 dependencies

Last updated 11 months agofrom:72f692e8c7. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-win-x86_64NOTEOct 23 2024
R-4.5-linux-x86_64NOTEOct 23 2024
R-4.4-win-x86_64NOTEOct 23 2024
R-4.4-mac-x86_64NOTEOct 23 2024
R-4.4-mac-aarch64NOTEOct 23 2024
R-4.3-win-x86_64NOTEOct 23 2024
R-4.3-mac-x86_64NOTEOct 23 2024
R-4.3-mac-aarch64NOTEOct 23 2024

Exports:check_MIPanalyzer_loadedexplore_filter_coverage_lociexplore_filter_coverage_samplesfilter_countsfilter_coverage_locifilter_coverage_samplesfilter_locifilter_loci_invariantfilter_overcountsfilter_samplesfilter_wsafget_genomic_distanceget_IB_mixtureget_IBS_distanceget_spatial_distanceget_wsafinbreeding_mleis.mipanalyzer_biallelicis.mipanalyzer_multialleliclonlat_to_bearingmipanalyzer_biallelic_to_vcfRmipanalyzer_filepca_wsafpcoa_genomic_distancePf_chrom_lengthsplot_coverageplot_distanceplot_mapplot_pcaplot_pca_contributionplot_pca_varianceplot_pcoaplot_wsafrbetabinomrdirichletsim_biallelicvcf_to_mipanalyzer_biallelicvcf_to_mipanalyzer_multiallelic

Dependencies:apeaskpassbase64encbslibcachemcliclustercodacolorspacecpp11crosstalkcurldata.tabledigestdotCall64dplyrevaluatefansifarverfastmapfieldsfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrmapsMASSMatrixmemoisememusemgcvmimemunsellnlmeopensslpermutepillarpinfsc50pkgconfigplotlyplyrpromisespurrrR6rappdirsrasterRColorBrewerRcppreshape2rlangrmarkdownrworldmapsassscalesspspamstringistringrsysterratibbletidyrtidyselecttinytexutf8vcfRvctrsveganviridisLitewithrxfunyaml

Analysis of population structure

Bob Verity

Rendered fromstructure_analysis.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2023-12-12
Started: 2023-12-12

Comparing genetic distances

Bob Verity

Rendered fromgenetic_distances.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2023-12-12
Started: 2023-12-12

Installation

Rendered frominstallation.Rmdusingknitr::knitron Oct 23 2024.

Last update: 2023-12-12
Started: 2023-12-11

Reading in and filtering data

Bob Verity

Rendered fromfiltering_data.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2023-12-12
Started: 2023-12-11

Readme and manuals

Help Manual

Help pageTopics
Check that MIPanalyzer package has loaded successfullycheck_MIPanalyzer_loaded
Explore locus coverage prior to filteringexplore_filter_coverage_loci
Explore sample coverage prior to filteringexplore_filter_coverage_samples
Filter alleles based on raw countsfilter_counts
Filter loci based on coveragefilter_coverage_loci
Filter samples based on coveragefilter_coverage_samples
Filter out some locifilter_loci
Filter loci to drop invariant sitesfilter_loci_invariant
Filter out over-countsfilter_overcounts
Filter out some samplesfilter_samples
Filter alleles based on within-sample allele frequenciesfilter_wsaf
Get genomic distance between samplesget_genomic_distance
Get identity by mixtureget_IB_mixture
Get identity by state (IBS) distanceget_IBS_distance
Get great circle distance between spatial pointsget_spatial_distance
Get within-sample allele frequenciesget_wsaf
Estimate pairwise inbreeding coefficient F by maximum likelihoodinbreeding_mle
Determine if object is of class mipanalyzer_biallelicis.mipanalyzer_biallelic
Determine if object is of class mipanalyzer_multiallelicis.mipanalyzer_multiallelic
Calculate great circle distance and bearing between coordinateslonlat_to_bearing
MIPanalyzerMIPanalyzer-package MIPanalyzer
Converts a MIPanalyzer biallelic object to vcfRmipanalyzer_biallelic_to_vcfR
Load system filemipanalyzer_file
PCA of within-sample allele frequenciespca_wsaf
PCoA of genomic distances between samplespcoa_genomic_distance
Get dataframe of P.falciparum chromosome lengthsPf_chrom_lengths
Plot coverage matrixplot_coverage
Plot a distance matrixplot_distance
Produce ggplot mapplot_map
Plot PCAplot_pca
Plot PCA contribution of each variableplot_pca_contribution
Plot variance explained by PCA componentsplot_pca_variance
Plot PCoAplot_pcoa
Plot within-sample allele frequenciesplot_wsaf
Custom print function for class mipanalyzer_biallelicprint.mipanalyzer_biallelic
Custom print function for class mipanalyzer_multiallelicprint.mipanalyzer_multiallelic
Draw from Beta-binomial distributionrbetabinom
Draw from Dirichlet distributionrdirichlet
Simulate biallelic datasim_biallelic
Print summary for class mipanalyzer_biallelicsummary.mipanalyzer_biallelic
Print summary for class mipanalyzer_multiallelicsummary.mipanalyzer_multiallelic
Convert vcf to biallelic mipanalyzer data classvcf_to_mipanalyzer_biallelic
Convert vcf to multiallelic mipanalyzer data classvcf_to_mipanalyzer_multiallelic