October 2014

The biomaRt package

October 2, 2014 | January

The biomaRt package allows to query the gigantic ensembl data base directly from R. Since it happens only once in a while, I find myself reading the biomaRt vignette every time I’m using it. Here are the crucial points for the most common application. The data frames f and ... [Read more...]

Le ali della spesa pubblica

October 2, 2014 | Salvino A. Salvaggio

Salvino A. Salvaggio, PhDA Carlo Cottarelli, economista italiano incaricato nel novembre 2013 di tagliare la spesa pubblica, il governo italiano ha tagliato le ali nell'ottobre 2014. Archiviata, benche' largamente incompiuta, la spending review, all'It... [Read more...]

Vector Search vs. Binary Search

October 1, 2014 | statcompute

[This article was first published on Yet Another Blog in Statistical Computing » S+/R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don't. # REFERENCE: # user2014.stat.ucla.edu/files/tutorial_Matt.pdf pkgs <- c('data.table', 'rbenchmark') lapply(pkgs, require, character.only = T) load('2008.Rdata') dt <- data.table(data) benchmark(replications = 10, order = "elapsed", vector_search = { test1 <- dt[ArrTime == 1500 & Origin == 'ABE', ] }, binary_search = { setkey(dt, ArrTime, Origin) test2 <- dt[.(1500, 'ABE'), ] } ) # test replications elapsed relative user.self sys.self user.child # 2 binary_search 10 0.335 1.000 0.311 0.023 0 # 1 vector_search 10 7.245 21.627 7.102 0.131 0 To leave a comment for the author, please follow the link and comment on their blog: Yet Another Blog in Statistical Computing » S+/R. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job. Want to share your content on R-bloggers? click here if you have a blog, or here if you don't. [Read more...]

New York Times approachably describes Bayesian Statistics

October 1, 2014 | David Smith

The New York Times published an article of interest to statisticians the other day: "The Odds, Continually Updated". Surprisingly for a general-audience newspaper, this article goes into the the distinctions between Bayesian and frequentist statistics, and does so in a very approachable way. Here's an excerpt: The essence of the ... [Read more...]

Got a ticket for the runoff?

October 1, 2014 | Daniel Marcelino

This is one of the very last posting before the election next Sunday. So far, the only certainty is the runoff ticket of the incumbent candidate, Dilma Rousseff (PT). The runner up candidates, the environmentalist Marina Silva (PSB) and the Social Democrat Aecio Neves are walking to a neck-and-neck dispute ... [Read more...]

Working with NIfTI images in R

October 1, 2014 | strictlystat

The oro.nifti package is awesome for NeuRoimaging (couldn't help myself). It has functions to read/write images, introduces the S4 nifti class, and has useful plotting functions. There are some limitations and some gotchas that are important to discuss if you are working with these objects in R. Dataset ... [Read more...]

multiple annotation in ChIPseeker

October 1, 2014 | R on Guangchuang Yu

Nearest gene annotation Almost all annotation software calculate the distance of a peak to the nearest TSS and assign the peak to that gene. This can be misleading, as binding sites might be located between two start sites of different genes or hit different genes which have the same TSS ... [Read more...]

Transparent hurricane paths in R

October 1, 2014 | Robert

Arthur Charpentier has written a really nice blog post about obtaining hurricane tracks and plotting them. He then goes on to do other clever Markov process models, but as a dataviz guy who knows almost nothing about meteorology, I want to … Continue reading → [Read more...]
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