Man pages for bmansfeld/QTLseqR
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

countSNPs_cppCount number of SNPs within a sliding window
FilterSNPsFilter SNPs based on read depth and quality
getFDRThresholdFind false discovery rate threshold
getGCalculates the G statistic
getPvalsNon-parametric estimation of the null distribution of G'
getQTLTableExport a summarized table of QTL
getSigRegionsReturn SNPs in significant regions
ImportFromGATKImports SNP data from GATK VariablesToTable output
plotGprimeDistPlots Gprime distribution
plotQTLStatsPlots different paramaters for QTL identification
plotSimulatedThresholdsPlots simulation data for QTLseq analysis
runGprimeAnalysisIdentify QTL using a smoothed G statistic
runQTLseqAnalysisCalculates delta SNP confidence intervals for QTLseq analysis
simulateAlleleFreqRandomly calculates an alternate allele frequency within a...
simulateConfIntSimulation of delta SPP index confidence intervals
simulateSNPindexSimulates a delta SNP-index with replication
tricubeStatCalculate tricube weighted statistics for each SNP
bmansfeld/QTLseqR documentation built on March 23, 2018, 7:01 a.m.