QTL_BSA-Sorghum
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  • QTL_BSA_Crop_Varieties
    • QTLSorghum
      • For more detailed instructions please read the vignettehere
      • For updates read the NEWS.md
    • Installation
      • Package Dependencies
    • Citation
      • Abstract
    • Examples:
      • Load/install libraries
      • Set the Working Directory
    • Pre-Filtering Rules
    • Importing Data
      • importFromVCF
      • importFromGATK
    • Input Fields ImportFromVCF
      • importFromTable
      • Inspect Header
    • Input Fields ImportFromGATK
      • importFromTable
      • Histograms
    • filterSNPs
    • runGprimeAnalysis_MH
    • plotGprimeDist_MH
    • runQTLseqAnalysis_MH
      • Plot G Statistic Distribution as a Histogram
    • plotQTLStats
      • nSNPs
      • Gprime
      • deltaSNP
      • negLog10Pval
      • Gprime Subset
    • rMVP Package
      • SNP Densities
    • Export summary CSV
      • Preview the Summary QTL
    • Theory
      • Contigency Table
      • Obs_Allel_Freq
      • Obs_Allele_Freq2
      • Total Coverage and Expected Allelic Frequencies
    • Theory and Analytical Framework of Sampling from BSA
      • Binomial Sampling
      • High Bulk
      • Low Bulk
      • Conditional Distribution of n1 given realized average frequency
      • Observed n1
      • Conditional Distribution of n2 given realized average frequency
      • Observed n2
      • Conditional Distribution of n3 given realized average frequency
      • Observed n3
      • Conditional Distribution of n4 given realized average frequency
      • Observed n4
      • An interdependentaly observed relationship between G and Gprime
  • QTL_Rice_Cold_Tolerance
    • QTL-Rice-Cold-Tolerance
      • For more detailed instructions please read the vignettehere
      • For updates read the NEWS.md
    • Installation
      • Package Dependencies
    • Citation
      • Abstract
    • Examples:
      • Load/install libraries
      • Set the Working Directory
    • Pre-Filtering Rules
    • The Lonely Parser
    • Import Data
      • importFromTable
      • importFromVCF
      • GATK
    • Input Fields
    • importFromTable
      • Histograms
    • filterSNPs
    • runGprimeAnalysis_MH
    • plotGprimeDist_MH
    • runQTLseqAnalysis_MH
      • Plot G Statistic Distribution as a Histogram
    • plotQTLStats
      • nSNPs
      • Gprime
      • deltaSNP
      • negLog10Pval
      • Gprime Subset
    • rMVP Package
      • SNP Densities
    • Export summary CSV
      • Preview the Summary QTL
    • Theory
      • Contigency Table
      • Obs_Allel_Freq
      • Obs_Allele_Freq2
      • Total Coverage and Expected Allelic Frequencies
    • Chromosomal Sampling Theory and an Analytical Framework with respect to Bulk Segregant Analysis
      • Binomial Sampling
      • Low Bulk
      • High Bulk
      • Conditional Distribution of n1 given realized average frequency
      • Observed n1
      • Conditional Distribution of n2 given realized average frequency
      • Observed n2
      • Conditional Distribution of n3 given realized average frequency
      • Observed n3
      • Conditional Distribution of n4 given realized average frequency
      • Observed n4
      • An interdependentaly observed relationship between G and Gprime
QTL_BSA-Sorghum
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