Package: poolHelper 1.1.0.9000

João Carvalho

poolHelper: Simulates Pooled Sequencing Genetic Data

Simulates pooled sequencing data under a variety of conditions. Also allows for the evaluation of the average absolute difference between allele frequencies computed from genotypes and those computed from pooled data. Carvalho et al., (2022) <doi:10.1101/2023.01.20.524733>.

Authors:João Carvalho [aut, cre], Vítor Sousa [aut]

poolHelper_1.1.0.9000.tar.gz
poolHelper_1.1.0.9000.zip(r-4.7-any)poolHelper_1.1.0.9000.zip(r-4.6-any)poolHelper_1.1.0.9000.zip(r-4.5-any)
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poolHelper_1.1.0.9000.tar.gz(r-4.7-any)poolHelper_1.1.0.9000.tar.gz(r-4.6-any)
poolHelper_1.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
poolHelper/json (API)

# Install 'poolHelper' in R:

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

Bug tracker:https://github.com/joao-mcarvalho/poolhelper/issues

On CRAN:

3.70 score 5 scripts 249 downloads 43 exports 13 dependencies

Last updated from:25cc7f71b7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	124
source / vignettes	OK	250
linux-release	OK	119
macos-release	OK	204
macos-oldrel	OK	186
windows-devel	OK	94
windows-release	OK	78
windows-oldrel	OK	78
wasm-release	OK	96

Exports:calculatePi computeReference errorHet Expected_Het ExpHet_site filterMinor filterPool findMinor forcePool GetGenotypes getNumReadsR_vector hap2geno haplo.fix Ifreqs indProbs indReads maeFreqs maeHet maePool mymae numberReference numberReferencePop Pfreqs pool2sync pool2vcf poolPops poolProbs poolReads popReads popsReads remove_by_reads remove_by_reads_matrix removeSites run_scrm simPoolseq simReads simulateCoverage splitMatrix strg2sync strg2vcf vcfinfo vcfloci vcflocus

Dependencies:coda lattice MASS Matrix MatrixModels mcmc MCMCpack Metrics quantreg Rcpp scrm SparseM survival

Vignette for the poolHelper package

Rendered frompoolHelper.Rmdusingknitr::rmarkdown

Last update: 2023-06-30
Started: 2023-06-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate population frequency at each SNP	calculatePi
Compute the number of reference reads over a matrix	computeReference
Average absolute difference between expected heterozygosity	errorHet
Define major and minor alleles	findMinor
Compute the number of reference reads	getNumReadsR_vector
Compute allele frequencies from genotypes	Ifreqs
Probability of contribution of each individual	indProbs
Reads contributed by each individual	indReads
Average absolute difference between allele frequencies computed from genotypes and from Pool-seq data	maeFreqs
Average absolute difference between the expected heterozygosity computed from genotypes and from Pool-seq data	maeHet
Average absolute difference between allele frequencies	maePool
Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq data	mymae
Compute the number of reference reads for multiple populations	numberReferencePop
Compute allele frequencies from pooled sequencing data	Pfreqs
Create 'synchronized' file from Pool-seq data	pool2sync
Create VCF file from Pool-seq data	pool2vcf
Create Pooled DNA sequencing data for multiple populations	poolPops
Probability of contribution of each pool	poolProbs
Reads contributed by each pool	poolReads
Compute number of reads for each individual and across all sites	popReads
Simulate total number of reads for multiple populations	popsReads
Apply a coverage-based filter over a list	remove_by_reads
Apply a coverage-based filter to a matrix	remove_by_reads_matrix
Apply a minor allele reads threshold	removeSites
Simulate a single population	run_scrm
Simulate Pool-seq data	simPoolseq
Simulate coverage at a single locus	simReads
Simulate total number of reads per site	simulateCoverage