myfuncs-package: My collection of utility functions

myfuncs-packageR Documentation

My collection of utility functions

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 <january.weiner@gmail.com>


january3/myfuncs documentation built on Jan. 16, 2025, 8:37 p.m.