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Package: moimix 0.0.2.9001

"Stuart Lee"

moimix: Estimating mulitplicity of infection from high-throughput sequencing data

Evaluate multiplicity of infection (MOI) of organisms using binomial mixture models and other population genetics methods. moimix can be used to simulate single nucleotide variant (SNV) data from samples with known MOI.

Authors:"Stuart Lee" [aut, cre]

moimix_0.0.2.9001.tar.gz
moimix_0.0.2.9001.zip(r-4.7-any)moimix_0.0.2.9001.zip(r-4.6-any)moimix_0.0.2.9001.zip(r-4.5-any)
moimix_0.0.2.9001.tgz(r-4.6-any)moimix_0.0.2.9001.tgz(r-4.5-any)
moimix_0.0.2.9001.tar.gz(r-4.7-any)moimix_0.0.2.9001.tar.gz(r-4.6-any)
moimix_0.0.2.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
moimix/json (API)

# Install 'moimix' in R:

install.packages('moimix', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

maf_summary - Minor Allele Frequenies of ~ 30,000 Plasmodium falciparum SNPs.

On CRAN:

3.65 score 5 stars 18 scripts 33 exports 100 dependencies

Last updated from:802eaf1fab. Checks:7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel	NOTE	257
source / vignettes	OK	288
linux-release	NOTE	255
macos-release	NOTE	177
macos-oldrel	NOTE	205
windows-devel	NOTE	206
windows-release	NOTE	198
windows-oldrel	NOTE	147
wasm-release	OK	135

Exports:alleleCounts bafMatrix barcodes binommix callMajor coverageBySample coverageBySNP dtbeta dtexp extractBarcode extractPED generateWindows getBarcodeVariants getCoordinates getDosage getFws getGATKInfo getHeterozygosity getHeterozygosityBySample getMAF getMSE getTheta infomat lltexp mleTexp mse perSiteAlleleCoverage perSiteCoverageBySample perSiteCoverageBySNP readEstMOI rtexp seMM simulateMOI

Dependencies:backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 boot broom cli clipr coda codetools cpp11 crayon data.table digest dplyr farver flexmix forcats foreach formatR formula.tools futile.logger futile.options gdsfmt generics GenomicRanges glmnet glue GWASExactHW haven hms IRanges iterators jomo labeling lambda.r lattice lifecycle lme4 logistf magrittr MASS Matrix MatrixModels mcmc MCMCpack mgcv mice minqa mitml modeltools nlme nloptr nnet numDeriv operator.tools ordinal pan pillar pkgconfig prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack readr reformulas rlang rpart S4Vectors scales SeqArray Seqinfo SeqVarTools shape snow SparseM stringi stringr survival tibble tidyr tidyselect tzdb ucminf utf8 vctrs viridisLite vroom withr XVector

Introduction to moimix package

Key functions in moimix | Data Formats | Converting a VCF to GDS format | Case study: Plasmodium falciparum isolates from The Gambia. | Estimating the BAF matrix | Estimating MOI with binommix | Estimating MOI with $F_{ws}$ | References | Session Info

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2020-04-13
Started: 2016-02-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Return allele counts from a genofile based on read counts	alleleCounts
Compute B-allele frequency spectrum genome-wide	bafMatrix
Generate GenomicRanges object from GDS file	barcodes
Fit binomial mixture model on coverage data	binommix
CDF for binomial mixture model	binommixCDF
Get major allele calls for isolates from BAF matrix	callMajor
Generate Confidence Intervals for parameter estimates using estimated Fisher Information Matrix	ciMM
SNP coverage rates by sample thresholds	coverageBySample
Sample coverage rates by SNP thresholds	coverageBySNP
Truncated beta distribution	dtbeta ptbeta qtbeta rtbeta
Truncated exponential distrubition	dtexp lltexp mleTexp
Extract barcode for use in COIL program	extractBarcode
Extract PED files from gds	extractPED
Plasmodium falciparum SNV data from Gambia.	gambian_isolates
Construct non-overlapping Genomic Windows by Chromosome	generateWindows
Helper functions for extracting variant IDs corresponding to previously published barcodes.	getBarcodeVariants
Helper function for producing data frame of genomic coordinates	getCoordinates
Helper function for producing matrix of allele dosages	getDosage
Compute Fws within-host diversity statistic	getFws
Get GATK info tags	getGATKInfo
Compute population level heterozygosity	getHeterozygosity
Compute heterozygosity by sample	getHeterozygosityBySample
Compute minor allele frequency	getMAF
Model assessment for fitted model using MSE	getMSE
Return estimated model parameters	getTheta
Fisher Information Approximation	infomat
Minor Allele Frequenies of ~ 30,000 Plasmodium falciparum SNPs.	maf_summary
Evaluate muliplicity of infection in malaria parasites	moimix
Mean Square Error for binomial mixture model	mse
Compute per site per sample coverage	perSiteAlleleCoverage
Compute per variant depth accross all samples.	perSiteCoverage
Compute the proportion of samples covered up any number of bases	perSiteCoverageBySample
Compute proportion of SNPs covered up to a lower bound of bases within each sample.	perSiteCoverageBySNP
Plot bafMatrix object	plot.bafMatrix
Parse estMOI log files in a directory into tidy data frame	readEstMOI
Truncated exponential distribution random number generation	rtexp
Generate iid binomial mixture random variables for testing EM implementation	sampleMM
sum number of samples/snps meeting coverage threshold scaled by total number of SNPs/proportions	scaledProportion
Compute standard errors for mixture model parameter estimates	seMM
Simple simulation of MOI SNV data	simulateMOI