{
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  "Package": "poolHelper",
  "Title": "Simulates Pooled Sequencing Genetic Data",
  "Version": "1.1.0.9000",
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  "Description": "Simulates pooled sequencing data under a variety of\nconditions. Also allows for the evaluation of the average\nabsolute difference between allele frequencies computed from\ngenotypes and those computed from pooled data. Carvalho et al.,\n(2022) <doi:10.1101/2023.01.20.524733>.",
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  "Repository": "https://vsousa.r-universe.dev",
  "Date/Publication": "2023-06-30 16:22:57 UTC",
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      "date": "2023-01-25"
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    "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"
  ],
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    {
      "page": "calculatePi",
      "title": "Calculate population frequency at each SNP",
      "topics": [
        "calculatePi"
      ]
    },
    {
      "page": "computeReference",
      "title": "Compute the number of reference reads over a matrix",
      "topics": [
        "computeReference"
      ]
    },
    {
      "page": "errorHet",
      "title": "Average absolute difference between expected heterozygosity",
      "topics": [
        "errorHet"
      ]
    },
    {
      "page": "findMinor",
      "title": "Define major and minor alleles",
      "topics": [
        "findMinor"
      ]
    },
    {
      "page": "getNumReadsR_vector",
      "title": "Compute the number of reference reads",
      "topics": [
        "getNumReadsR_vector"
      ]
    },
    {
      "page": "Ifreqs",
      "title": "Compute allele frequencies from genotypes",
      "topics": [
        "Ifreqs"
      ]
    },
    {
      "page": "indProbs",
      "title": "Probability of contribution of each individual",
      "topics": [
        "indProbs"
      ]
    },
    {
      "page": "indReads",
      "title": "Reads contributed by each individual",
      "topics": [
        "indReads"
      ]
    },
    {
      "page": "maeFreqs",
      "title": "Average absolute difference between allele frequencies computed from genotypes and from Pool-seq data",
      "topics": [
        "maeFreqs"
      ]
    },
    {
      "page": "maeHet",
      "title": "Average absolute difference between the expected heterozygosity computed from genotypes and from Pool-seq data",
      "topics": [
        "maeHet"
      ]
    },
    {
      "page": "maePool",
      "title": "Average absolute difference between allele frequencies",
      "topics": [
        "maePool"
      ]
    },
    {
      "page": "mymae",
      "title": "Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq data",
      "topics": [
        "mymae"
      ]
    },
    {
      "page": "numberReferencePop",
      "title": "Compute the number of reference reads for multiple populations",
      "topics": [
        "numberReferencePop"
      ]
    },
    {
      "page": "Pfreqs",
      "title": "Compute allele frequencies from pooled sequencing data",
      "topics": [
        "Pfreqs"
      ]
    },
    {
      "page": "pool2sync",
      "title": "Create 'synchronized' file from Pool-seq data",
      "topics": [
        "pool2sync"
      ]
    },
    {
      "page": "pool2vcf",
      "title": "Create VCF file from Pool-seq data",
      "topics": [
        "pool2vcf"
      ]
    },
    {
      "page": "poolPops",
      "title": "Create Pooled DNA sequencing data for multiple populations",
      "topics": [
        "poolPops"
      ]
    },
    {
      "page": "poolProbs",
      "title": "Probability of contribution of each pool",
      "topics": [
        "poolProbs"
      ]
    },
    {
      "page": "poolReads",
      "title": "Reads contributed by each pool",
      "topics": [
        "poolReads"
      ]
    },
    {
      "page": "popReads",
      "title": "Compute number of reads for each individual and across all sites",
      "topics": [
        "popReads"
      ]
    },
    {
      "page": "popsReads",
      "title": "Simulate total number of reads for multiple populations",
      "topics": [
        "popsReads"
      ]
    },
    {
      "page": "remove_by_reads",
      "title": "Apply a coverage-based filter over a list",
      "topics": [
        "remove_by_reads"
      ]
    },
    {
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      "title": "Apply a coverage-based filter to a matrix",
      "topics": [
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      ]
    },
    {
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      "title": "Apply a minor allele reads threshold",
      "topics": [
        "removeSites"
      ]
    },
    {
      "page": "run_scrm",
      "title": "Simulate a single population",
      "topics": [
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      ]
    },
    {
      "page": "simPoolseq",
      "title": "Simulate Pool-seq data",
      "topics": [
        "simPoolseq"
      ]
    },
    {
      "page": "simReads",
      "title": "Simulate coverage at a single locus",
      "topics": [
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      ]
    },
    {
      "page": "simulateCoverage",
      "title": "Simulate total number of reads per site",
      "topics": [
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      ]
    }
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  "_rundeps": [
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        "introduction",
        "Basic functionality",
        "Pool-seq experimental design",
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        "What pool size should I use?",
        "How to test different combinations?",
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      "created": "2023-06-30 13:40:51",
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