== Write to the clipboard == Ever produce a list that you want to take somewhere else outside of R without having to write it to a file? Use the ClipBoard! The only annoying thing is that you have to write them as a character vector. {{{ # get some random numbers x <- runif(5) # write them to the clipboard writeClipboard(as.character(x)) }}} To move tables of data, use the write.table function: {{{ mytable <- matrix(1:100, ncol=10, nrow=10) write.table(mytable, "clipboard", sep="\t") # suppress row and column names write.table(mytable, "clipboard", sep="\t", row.names=FALSE, col.names=FALSE) }}} To move a column of numbers into R from other programs you can use the scan() function. For instance {{{ # bring a column of numbers from the clipboard into a vector x <- scan() # hit Paste, then Return # or use readClipboard x <- readClipboard() }}} == How to flatten a matrix in R == If you have a matrix or data frame where some of the rows have values that need to be averaged. There are a few ways to go about this. Imagine you have a table of gene expression values measured under various conditions. Each row of the table represents a gene, some of the rows represent replicate measurements of that gene. The gene name is found in the column "sys_id". Each column represents a different condition. To average the replicates you could do the following: Example 1: {{{ library(stats) mat <- aggregate(dat[, 2:5], list(dat$sys_id), mean) }}} Example 2: Create a factor with the column of gene names, then use that factor to apply a function to the values in each individual column, then recombine the columns into a dataframe or matrix. use tapply() tapply(data, factor, function) == Colors for Heatmaps == {{{ library(RColorBrewer) hmcol <- colorRampPalette(brewer.pal(10, "RdBu"))(256) }}} == Write lines to a file == {{{ # open a file connection fout <- file("filename", "w") # print stuff to the connection (usually as part of a loop) cat("some data", sep="\n", file=fout) # close the connection close(fout) }}} == Install package from bioconductor == {{{ source("http://bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") }}}