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
MIPanalyzer_1.1.0.zip(r-4.7-x86_64)MIPanalyzer_1.1.0.zip(r-4.7-arm64)MIPanalyzer_1.1.0.zip(r-4.6-x86_64)MIPanalyzer_1.1.0.zip(r-4.6-arm64)MIPanalyzer_1.1.0.zip(r-4.5-x86_64)
MIPanalyzer_1.1.0.tgz(r-4.6-x86_64)MIPanalyzer_1.1.0.tgz(r-4.6-arm64)MIPanalyzer_1.1.0.tgz(r-4.5-x86_64)MIPanalyzer_1.1.0.tgz(r-4.5-arm64)
MIPanalyzer_1.1.0.tar.gz(r-4.7-arm64)MIPanalyzer_1.1.0.tar.gz(r-4.7-x86_64)MIPanalyzer_1.1.0.tar.gz(r-4.6-arm64)MIPanalyzer_1.1.0.tar.gz(r-4.6-x86_64)
MIPanalyzer_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MIPanalyzer/json (API)

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

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

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

On CRAN:

Conda:

cpp

4.19 score 2 stars 39 scripts 38 exports 87 dependencies

Last updated from:72f692e8c7. Checks:13 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE254
linux-devel-x86_64NOTE267
source / vignettesOK312
linux-release-arm64NOTE227
linux-release-x86_64NOTE245
macos-release-arm64NOTE264
macos-release-x86_64NOTE509
macos-oldrel-arm64NOTE195
macos-oldrel-x86_64NOTE712
windows-devel-arm64NOTE350
windows-devel-x86_64NOTE300
windows-release-arm64NOTE339
windows-release-x86_64NOTE261
windows-oldrel-x86_64NOTE263
wasm-releaseOK170

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:apeaskpassbase64encbslibcachemcliclustercodacpp11crosstalkcurldata.tabledigestdotCall64dplyrevaluatefarverfastmapfieldsfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrmapsMASSMatrixmemoisememusemgcvmimenlmeopensslotelpermutepillarpinfsc50pkgconfigplotlyplyrpromisespurrrR6rappdirsrasterRColorBrewerRcppreshape2rlangrmarkdownrworldmapS7sassscalesspspamstringistringrsysterratibbletidyrtidyselecttinytexutf8vcfRvctrsveganviridisLitewithrxfunyaml

Analysis of population structure
Principal Component Analysis (PCA) | Principal Coordinates Analysis (PCoA) from genetic distances
Rendered fromstructure_analysis.Rmdusingknitr::rmarkdown

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

Comparing genetic distances
Estimating relatedness between samples | Comparing different distance metrics
Rendered fromgenetic_distances.Rmdusingknitr::rmarkdown

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

Installation
Installing Rcpp | Installing and loading MIPanalyzer
Rendered frominstallation.Rmdusingknitr::knitr

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

Reading in and filtering data
Reading in data and understanding the mipanalyzer_biallelic format | Filtering data based on coverage | Filtering based on other criteria
Rendered fromfiltering_data.Rmdusingknitr::rmarkdown

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