Man pages for jtlovell/qtlTools
Data Processing and Plotting in Association with R/qtl

calcCisCalculate all confidence intervals from a QTL model
covScanQTLFind the effect of candidate genes based on gene expression.
dropByDroponeDrop markers that significantly expand the genetic map.
dropSimilarMarkersMethod to improve a genetic map.
findGenecMFind the cM location of genes.
findGenesIntervalFind candidate genes for QTL.
geno2crossFormat a genotype matrix to a R/qtl readable file
inferMarkerPosFind the best mapping position for a marker
matchMarkerOrderOrient chromosomes to match some previously found marker...
meanScanMake a scanone plot of genotype means.
newLGRe-order markers and re-form linkage groups
plotGeneModelA plotting method for gene models
polygenicQTLRun rrBLUP polygenic inheritance on an R/qtl model
pullMapPull the genetic map and marker names
pullSigQTLMethod to summarize scanone results
qtlSignTestConduct the sign test for expression bias
qtlStatsExtract statistics from a QTL model
quantnormQuantile normalize vector of numeric data
reDoCrossRun a set of functions that improve the genetic map
repPickMarkerSubsetMethod to improve an estimated genetic map.
repRippleMethod to improve a genetic map.
scanone.GWERkScanone qtl analysis permitting GWERk analysis.
scanone.lmerConduct mixed effect QTL mapping.
scantwo.GWERkScanone qtl analysis permitting GWERk analysis.
segmentsOnMapVisualize the positions of QTL on a genetic map.
segmentsOnPeaksSingle QTL confidence intervals on LOD curves
splitTextSimplify strsplit functionality
stepwiseqtl.intstepwise qtl analysis forcing an interactive covariate
swGenotypeCall markers based on allelic imbalance.
theme_jtlsimple custom themes
theme_jtlbarsimple custom themes
tspOrderOrder markers within linkage groups
jtlovell/qtlTools documentation built on April 3, 2018, 7:54 a.m.