Array construction in R, Perl, and Python R:
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data |
Perl:
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@data = (1, 2, 3) @data[2..3] %hash = ('a' =>; 'b') $hash{a} |
Python:
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data = [1, 2, 3, 'a', 'b', 'c'] data[2:3] tuple = (1, 2, 3, 'a', 'b', 'c') # immutable dict = {'a': 'America', 'c': 'Canada'} dict['a'] |
Debugging R scripts with command line arguments. 1. Break up the script into two parts: one for reading the arguments, another one for the analysis. 2. Run R with *-args option. It enters the interactive R session. Example. R –args
showMethods() and selectMethod() to find the functions and sources of S3 object in R. http://tolstoy.newcastle.edu.au/R/help/05/09/12506.html
Shuffle sequences in DNASequenceSet. lapply() or sapply() return list. endoapply() returns the same data class, DNASequenceSet. It is way slower, though.
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shuffled.seqs <- endoapply(seqs, sample) |
For faster shuffling, look at the link. http://grokbase.com/t/r/bioconductor/133n8bw1f6/bioc-how-to-operate-on-a-dnastringset-object
Turn numeric into categorical data.
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AdultUCI[["age"]] <- ordered(cut(AdultUCI[["age"]], c(15,25,45,65,100)), labels = c("Young", "Middle-aged", "Senior", "Old")) |
Change the order of discrete axis. Generate a factor with reversed levels or use a new ggplot2 option. Examples. df$X1 = with(df, factor(X1, levels = rev(levels(X1)))) http://stackoverflow.com/questions/7418191/sorting-dotplot-factor-axis-in-ggplot Reverse the order of a discrete-valued axis Get the levels of the factor
Nested Tmux command. Screen (vim + gnu screen/tmux) is a great tool for vim that split the pane and send vim buffer to another pane. (Link: http://www.vim.org/scripts/script.php?script_id=2711) However, when used the plugin in tmux session, the tmux sessions are nested
Slopegraph in R. Slopegraph shows the change of the quantity or rank. Beautiful slopegraph example. http://www.drewconway.com/zia/ Theory of slopegraph. http://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0003nk An R and ggplot2 code example of slopegraph https://github.com/leondutoit/slopegraph/blob/master/slopegraph. R Example code. Generate sample data
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a <- data.frame(go = LETTERS[1:10], enrich = runif(10, 0, 10)) b <- data.frame(go = LETTERS[1:10], enrich = runif(10, 0, 10)) a <- cbind(a, status ='before') b <- cbind(b, status = 'after') ab.melt <- rbind(a, b) |
Add an offset column
R function matching a function argument against candidate values. match.arg(arg, choices, several.ok = FALSE) arg = match.arg(arg)
How to rank data in R. rank(a) Then how to rank the data in reverse order? rand(-a)