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
importFromTableImport SNP data from a delimited file
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 Sept. 9, 2018, 12:17 p.m.