| all_ablines | Plot vertical, horizontal and diagonal ablines |
| arrayplot | Show an image based on row/column information |
| auc | shorthand to return the AUC calculated by pROC |
| auc.pval | shorthand to return the the p-value of AUC calculated by pROC |
| balanceset | Balance samples |
| browse | Browse a large object |
| calcDif | Create a "difference" gene expression set |
| catf | Shortcut with sprintf |
| cc | Smart counters for rmarkdown |
| centers.predict | useful for predicting cluster membership from cmeans and... |
| clustCompPlot | compare different clusters in an overview plot |
| clustplot | first attempt at pca/clustering plot (not working?) |
| clustsizes | calculate sizes of clusters |
| combineTopTableAll | Convert a topTableAll results by gene ID |
| confuMat | Calculate a confusion matrix |
| copyan | Annotated PDF copy of the graph produced |
| dfsearch | Search through a data frame |
| ding | Show a zenity dialog "Calculation complete" |
| distVI | Calculate the variation of information distances |
| dmtx2graph | Convert a distance matrix to an undirected graph |
| dotpair | A variant of the pairs plot |
| factorsummary | Convert columns of a data.frame to factors and show summary |
| fastboxplot | A boxplot consisting of lines only |
| fig_label | Create a label at the top left of the graphics device |
| genePairs | Pairs plot using smoothScatter |
| getGOrilla | Wrapper to run the online GO service GOrilla |
| getsubsets | Sample a number of samples by factor levels |
| grep.df | Quick grep through all columns of a data frame |
| likelihood.test | Likelihood test |
| linepairs | Beeswarm with lines linking pairs |
| lineq | Parameters of a line drawn on a plot |
| lp | Send current graph to printer. |
| mkdesign | Quickly make a design |
| MSD | Calculate MSD based on logFC and CI |
| mybarplot | A variant box and whiskers plot |
| myfaces | Chernoff faces |
| myfuncs-package | My collection of utility functions |
| myfuncs.reload | Reload the myfuncs package |
| mykfold | kfold cross-validation with additional features |
| myloess.sd | Local Polynomial Regression Fitting with Variability bands |
| myloo | leave one out cross-validation with additional functions |
| mypalette | A nice, pastel color palette |
| myPlotDensities | Alternative to plotDensities from the limma package. |
| na.lomf | Last observation moved forward |
| normtosel | Standarization using a subset of the data |
| os | Report memory usage |
| pairedLOO | RF LOO removing whole group of subjects |
| pairedswarm | Beeswarm with lines linking pairs |
| pca2var | Calculate the variance explained for prcomp objects |
| pcaR2 | Calculate R-squared for a matrix or principal components |
| pcaR2plot | Automatic R2 plot |
| plotGenes | Simple function to plot gene expression |
| plotMyloess | Plot an object from myloess.sd |
| plotROCseries | Plot a series of ROCs |
| prcomp2 | A wrapper around prcomp |
| prconvert | Convert RF votes to plottable object |
| pval2str | Convert a p-value to a character corresponding to p-value... |
| qval2signedqval | Change q values to logarithmized signed q values |
| repsapply | A more general version of avereps |
| rf2pr | Convert random forest to format suitable for rocplot() |
| rg2csv | Save an RG object as CSV files |
| rocformat | Format AUC from roc() function |
| rocplot | Calculate and show ROC curve |
| rocseries_boxplot | plot a series of ROC prediction objects as boxplot |
| rocseries_table | Return a table with AUC for each prediction in a series |
| runSPIA | wrapper for the spia function. |
| saveAsCLS | Write pheno data as braindead CLS format |
| saveAsGCT | Write expression data in the braindead GCT format |
| save.xlsx | Save multiple objects to an excel file |
| sdbar | Draw whiskers on a plot |
| setColnames | Return the object with colnames set |
| setdiff | Set difference operator |
| setEdgeAttr | set Edge attributes in an Rgraphviz graph |
| shortcuts | Shortcuts for common functions |
| show.color | Shows a rectangle colored by that color |
| showgene | A combined beeswarm / boxplot |
| showGraph | Call RCytoscape functions to display a graph |
| simpleGOhyper | simple alternative to hyperGTest |
| smoothPalette | Create a gradient corresponding to a numeric vector |
| sortby | Shortcuts for sorting data frames |
| static_cache | Create a static cache at the specific path |
| topTableAll | Create a topTable for all coefficients in a limma fit object |
| ttmake | Create a topTable for limma with "msd" based on confidence... |
| ttplot | beeswarm for a top table (result of topTableAll) plot |
| ttsummary | Print a summary of a top table. |
| volcano | volcano plot |
| whatabout | Inteligently find significant coefficients for a gene |
| xclip | Copy a few history lines to the X primary clipboard |
| xpredict | Cross predict from one data set to another |
| xpredict.nvar | Determine optimal number of variables |
| zz | Save history and data image |
