myfuncs-package: My collection of utility functions

In january3/myfuncs: loads a few functions I often need

Description

A collection of utility functions

Details

A collection of utility functions

Shortcuts

• catf and printf implement printf() like functions

• os display memory usage

• shortcuts: l, h and p: wrappers for length, head and paste

• msd and ss mean and sd; sum of squares

• zz save everything

• myfuncs.reload reload the myfuncs package

Graphics and plotting

• all.ablines Draw three lines (horizontal at 0, vertical at 0, and diagonal)

• arrayplot Show image representation of a microarray

• showgene beeswarm + boxplot for a gene

• myfaces My version of Chernoff faces

• plotGenes Show expression for a number of genes in all arrays

• dotpair A version of pairs showing also correlation coefficients

• genePairs A version of pairs showing also correlation coefficients for large numbers of data points (using smoothScatter)

• myPlotDensities A replacement for plotDensities from limma for single-color arrays and for coloring array groups

• pairedswarm Beeswarm with lines linking pairs

• clustCompPlot compare different clusterings in an overview plot

• mypalette Nice color palette

• pcaR2plot Calculate and visualize PCA regression

• ttplot Plot a top table

• copyan Produce an annotated PDF copy of a plot

Analysis

• getGOrilla run GOrilla from R

• topTableAll produce a topTable-like output for all contrasts in a fit object

• ttmake produce a topTable-like output including the msd measure

• confuMat confusion matrix based on reality vs predictions

Data manipulation

• calcDif calculate pair differences in a limma object (for paired samples analysis)

• grep.df Grep all columns of a data frame

• repsapply general version of avereps

Others

• centers.predict

• clustsizes

• likelihood.test

• lineq

• matrixReshuffle

• pca2var

• pvals

• rfvalid

• ringfence

• smoothPalette

• twofacreshape

Author(s)

January Weiner <[e-mail]>

january3/myfuncs documentation built on April 1, 2020, 4:42 a.m.