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
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poolHelper.pdf |poolHelper.html✨
poolHelper/json (API)
NEWS

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

Peer review:

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

On CRAN:

43 exports 0.93 score 13 dependencies 1 dependents 3 scripts 249 downloads

Last updated 1 years agofrom:25cc7f71b7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winOKAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports:calculatePicomputeReferenceerrorHetExpected_HetExpHet_sitefilterMinorfilterPoolfindMinorforcePoolGetGenotypesgetNumReadsR_vectorhap2genohaplo.fixIfreqsindProbsindReadsmaeFreqsmaeHetmaePoolmymaenumberReferencenumberReferencePopPfreqspool2syncpool2vcfpoolPopspoolProbspoolReadspopReadspopsReadsremove_by_readsremove_by_reads_matrixremoveSitesrun_scrmsimPoolseqsimReadssimulateCoveragesplitMatrixstrg2syncstrg2vcfvcfinfovcflocivcflocus

Dependencies:codalatticeMASSMatrixMatrixModelsmcmcMCMCpackMetricsquantregRcppscrmSparseMsurvival

Vignette for the poolHelper package

Rendered frompoolHelper.Rmdusingknitr::rmarkdownon Aug 28 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Calculate population frequency at each SNPcalculatePi
Compute the number of reference reads over a matrixcomputeReference
Average absolute difference between expected heterozygosityerrorHet
Define major and minor allelesfindMinor
Compute the number of reference readsgetNumReadsR_vector
Compute allele frequencies from genotypesIfreqs
Probability of contribution of each individualindProbs
Reads contributed by each individualindReads
Average absolute difference between allele frequencies computed from genotypes and from Pool-seq datamaeFreqs
Average absolute difference between the expected heterozygosity computed from genotypes and from Pool-seq datamaeHet
Average absolute difference between allele frequenciesmaePool
Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq datamymae
Compute the number of reference reads for multiple populationsnumberReferencePop
Compute allele frequencies from pooled sequencing dataPfreqs
Create 'synchronized' file from Pool-seq datapool2sync
Create VCF file from Pool-seq datapool2vcf
Create Pooled DNA sequencing data for multiple populationspoolPops
Probability of contribution of each poolpoolProbs
Reads contributed by each poolpoolReads
Compute number of reads for each individual and across all sitespopReads
Simulate total number of reads for multiple populationspopsReads
Apply a coverage-based filter over a listremove_by_reads
Apply a coverage-based filter to a matrixremove_by_reads_matrix
Apply a minor allele reads thresholdremoveSites
Simulate a single populationrun_scrm
Simulate Pool-seq datasimPoolseq
Simulate coverage at a single locussimReads
Simulate total number of reads per sitesimulateCoverage