Man pages for january3/myfuncs
loads a few functions I often need

all_ablinesPlot vertical, horizontal and diagonal ablines
arrayplotShow an image based on row/column information
aucshorthand to return the AUC calculated by pROC
auc.pvalshorthand to return the the p-value of AUC calculated by pROC
balancesetBalance samples
browseBrowse a large object
calcDifCreate a "difference" gene expression set
catfShortcut with sprintf
ccSmart counters for rmarkdown
centers.predictuseful for predicting cluster membership from cmeans and...
clustCompPlotcompare different clusters in an overview plot
clustplotfirst attempt at pca/clustering plot (not working?)
clustsizescalculate sizes of clusters
combineTopTableAllConvert a topTableAll results by gene ID
confuMatCalculate a confusion matrix
copyanAnnotated PDF copy of the graph produced
dfsearchSearch through a data frame
dingShow a zenity dialog "Calculation complete"
distVICalculate the variation of information distances
dmtx2graphConvert a distance matrix to an undirected graph
dotpairA variant of the pairs plot
factorsummaryConvert columns of a data.frame to factors and show summary
fastboxplotA boxplot consisting of lines only
fig_labelCreate a label at the top left of the graphics device
genePairsPairs plot using smoothScatter
getGOrillaWrapper to run the online GO service GOrilla
getsubsetsSample a number of samples by factor levels
grep.dfQuick grep through all columns of a data frame
likelihood.testLikelihood test
linepairsBeeswarm with lines linking pairs
lineqParameters of a line drawn on a plot
lpSend current graph to printer.
mkdesignQuickly make a design
MSDCalculate MSD based on logFC and CI
mybarplotA variant box and whiskers plot
myfacesChernoff faces
myfuncs-packageMy collection of utility functions
myfuncs.reloadReload the myfuncs package
mykfoldkfold cross-validation with additional features
myloess.sdLocal Polynomial Regression Fitting with Variability bands
mylooleave one out cross-validation with additional functions
mypaletteA nice, pastel color palette
myPlotDensitiesAlternative to plotDensities from the limma package.
na.lomfLast observation moved forward
normtoselStandarization using a subset of the data
osReport memory usage
pairedLOORF LOO removing whole group of subjects
pairedswarmBeeswarm with lines linking pairs
pca2varCalculate the variance explained for prcomp objects
pcaR2Calculate R-squared for a matrix or principal components
pcaR2plotAutomatic R2 plot
plotGenesSimple function to plot gene expression
plotMyloessPlot an object from myloess.sd
plotROCseriesPlot a series of ROCs
prcomp2A wrapper around prcomp
prconvertConvert RF votes to plottable object
pval2strConvert a p-value to a character corresponding to p-value...
qval2signedqvalChange q values to logarithmized signed q values
repsapplyA more general version of avereps
rf2prConvert random forest to format suitable for rocplot()
rg2csvSave an RG object as CSV files
rocformatFormat AUC from roc() function
rocplotCalculate and show ROC curve
rocseries_boxplotplot a series of ROC prediction objects as boxplot
rocseries_tableReturn a table with AUC for each prediction in a series
runSPIAwrapper for the spia function.
saveAsCLSWrite pheno data as braindead CLS format
saveAsGCTWrite expression data in the braindead GCT format
save.xlsxSave multiple objects to an excel file
sdbarDraw whiskers on a plot
setColnamesReturn the object with colnames set
setdiffSet difference operator
setEdgeAttrset Edge attributes in an Rgraphviz graph
shortcutsShortcuts for common functions
show.colorShows a rectangle colored by that color
showgeneA combined beeswarm / boxplot
showGraphCall RCytoscape functions to display a graph
simpleGOhypersimple alternative to hyperGTest
smoothPaletteCreate a gradient corresponding to a numeric vector
sortbyShortcuts for sorting data frames
topTableAllCreate a topTable for all coefficients in a limma fit object
ttmakeCreate a topTable for limma with "msd" based on confidence...
ttplotbeeswarm for a top table (result of topTableAll) plot
ttsummaryPrint a summary of a top table.
whataboutInteligently find significant coefficients for a gene
xclipCopy a few history lines to the X primary clipboard
xpredictCross predict from one data set to another
xpredict.nvarDetermine optimal number of variables
zzSave history and data image
january3/myfuncs documentation built on Aug. 29, 2019, 9:12 p.m.