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| countSNPs_cpp | Count number of SNPs within a sliding window |
| filterSNPs | Filter SNPs based on read depth and quality |
| getFDRThreshold | Find false discovery rate threshold |
| getG | Calculates the G statistic |
| getPvals | Non-parametric estimation of the null distribution of G' |
| getQTLTable | Export a summarized table of QTL |
| getSigRegions | Return SNPs in significant regions |
| importFromGATK | Imports SNP data from GATK VariablesToTable output |
| importFromTable | Import SNP data from a delimited file |
| plotGprimeDist | Plots Gprime distribution |
| plotQTLStats | Plots different paramaters for QTL identification |
| plotSimulatedThresholds | Plots simulation data for QTLseq analysis |
| runGprimeAnalysis | Identify QTL using a smoothed G statistic |
| runQTLseqAnalysis | Calculates delta SNP confidence intervals for QTLseq analysis |
| simulateAlleleFreq | Randomly calculates an alternate allele frequency within a bulk |
| simulateConfInt | Simulation of delta SPP index confidence intervals |
| simulateSNPindex | Simulates a delta SNP-index with replication |
| tricubeStat | Calculate tricube weighted statistics for each SNP |