Man pages for jtlovell/qtlTools
Data Processing and Plotting in Association with R/qtl
| calcCis | Calculate all confidence intervals from a QTL model |
| covScanQTL | Find the effect of candidate genes based on gene expression. |
| dropByDropone | Drop markers that significantly expand the genetic map. |
| dropSimilarMarkers | Method to improve a genetic map. |
| findGenecM | Find the cM location of genes. |
| findGenesInterval | Find candidate genes for QTL. |
| geno2cross | Format a genotype matrix to a R/qtl readable file |
| inferMarkerPos | Find the best mapping position for a marker |
| matchMarkerOrder | Orient chromosomes to match some previously found marker... |
| meanScan | Make a scanone plot of genotype means. |
| newLG | Re-order markers and re-form linkage groups |
| plotGeneModel | A plotting method for gene models |
| polygenicQTL | Run rrBLUP polygenic inheritance on an R/qtl model |
| pullMap | Pull the genetic map and marker names |
| pullSigQTL | Method to summarize scanone results |
| qtlSignTest | Conduct the sign test for expression bias |
| qtlStats | Extract statistics from a QTL model |
| quantnorm | Quantile normalize vector of numeric data |
| reDoCross | Run a set of functions that improve the genetic map |
| repPickMarkerSubset | Method to improve an estimated genetic map. |
| repRipple | Method to improve a genetic map. |
| scanone.GWERk | Scanone qtl analysis permitting GWERk analysis. |
| scanone.lmer | Conduct mixed effect QTL mapping. |
| scantwo.GWERk | Scanone qtl analysis permitting GWERk analysis. |
| segmentsOnMap | Visualize the positions of QTL on a genetic map. |
| segmentsOnPeaks | Single QTL confidence intervals on LOD curves |
| splitText | Simplify strsplit functionality |
| stepwiseqtl.int | stepwise qtl analysis forcing an interactive covariate |
| swGenotype | Call markers based on allelic imbalance. |
| theme_jtl | simple custom themes |
| theme_jtlbar | simple custom themes |
| tspOrder | Order markers within linkage groups |
