| ath.churchill | Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites. |
| ath.gary | Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites. |
| ath.metab | Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites. |
| ath.metabolites | Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites. |
| ath.result | Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana. |
| basic.qc | Create quality control plots. |
| CTL | CTL - CTL mapping in experimental crosses |
| ctl | CTL - CTL mapping in experimental crosses |
| ctl.circle | Circleplot CTL on multiple traits |
| ctl.ctlmatrix | CTLhelper - Helper functions for CTL mapping |
| ctl.dcormatrix | CTLhelper - Helper functions for CTL mapping |
| ctl.lineplot | Lineplot CTL on multiple traits |
| ctl.load | ctl.load - Load CTLs calculated by the D2.0 version |
| ctl.name | CTLhelper - Helper functions for CTL mapping |
| ctl.names | CTLhelper - Helper functions for CTL mapping |
| ctl.qtlmatrix | CTLhelper - Helper functions for CTL mapping |
| ctl.qtlprofile | CTLhelper - Helper functions for CTL mapping |
| CTLmapping | CTLmapping - Scan for correlated trait loci (CTL) |
| CTLnetwork | CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits |
| CTLprofiles | CTLprofiles - Extract CTL interaction profiles |
| CTLregions | CTLregions - Get all significant interactions from a genome-wide CTLscan |
| CTLscan | CTLscan - Scan for Correlated Trait Locus (CTL) |
| CTLscan.cross | CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object) |
| CTLsignificant | CTLsignificant - Get all significant interactions from a genome-wide CTLscan |
| detect.peaks | detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold |
| hist.CTLobject | Plot histogram of CTL permutations |
| image.CTLobject | Plot genome-wide CTL on multiple traits |
| plot.CTLobject | Plot CTL curves or heatmaps |
| plot.CTLpermute | Differential correlation versus likelihood plotted in curves |
| plot.CTLscan | Plot CTL results as bar, line or GWAS plot. |
| plotTraits | plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus |
| print.CTLobject | Print the results of a CTL genome scan |
| print.CTLscan | Print the results of a single phenotype CTL scan |
| qtlimage | Plot a QTL heatmap of the phenotypes scanned by CTLscan |
| QTLmapping | QTLmapping - QTL mapping method for CTL analysis |
| scanSD | scanSD - Analyze the differences in Standard Deviation between genotypes between two traits |
| scanSD.cross | scanSD.cross - Analyze the differences in standard deviation between two traits at a certain genetic marker (R/qtl cross object) |
| scanSlopes | scanSlopes - Create a slope difference profile between two traits |
| scanSlopes.cross | scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object) |
| yeast.brem | Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions. |