Monthly Archives: November 2009

Show me the mean(ing)…

November 5, 2009
By
Show me the mean(ing)…

Well testing a bunch of samples for the largest population mean isn’t that common yet a simple test is at hand. Under the obvious title “The rank sum maximum test for the largest K population means” the test relies on the calculation of the sum of ranks under the combined sample of size , where

Read more »

Scivews-K got updated again

November 4, 2009
By
Scivews-K got updated again

With the recent update, I was able to get it working properly.Interestingly, while it works on my Vista 64-bit, it does not work on my Ubuntu 64-bit. I have no idea what is going on.

Read more »

R’s xtabs for total weighted read coverage

November 4, 2009
By

Samtools and its BioPerl wrapper Bio::DB:Sam prefer to give read coverage on a depth per base pair basis. This is typically an array of depths, one for every position that has at least one read aligned. OK, works for me. But how can we quickly see which targets (in my case transcripts) have the greatest total weighted read coverage...

Read more »

R’s xtabs for total weighted read coverage

November 4, 2009
By

Samtools and its BioPerl wrapper Bio::DB:Sam prefer to give read coverage on a depth per base pair basis. This is typically an array of depths, one for every position that has at least one read aligned. OK, works for me. But how can we quickly see which targets (in my case transcripts) have the greatest total weighted read coverage...

Read more »

Split, apply, and combine in R using PLYR

November 4, 2009
By

While flirting around with previously mentioned ggplot2 I came across an incredibly useful set of functions in the plyr package, made by Hadley Wickham, the same guy behind ggplot2.  If you've ever used MySQL before, think of "GROUP BY", but here you can arbitrarily apply any R function to splits of the data, or write one yourself. Imagine you have...

Read more »

LondonR tomorrow night

November 2, 2009
By

LondonR Date: Tuesday 3rd November Time: 6pm – 9.30pm Venue: Shooting Star Public house, 129 City Rd London, EC1, United Kingdom +44 20 7929 6818 Introduction: Richard Pugh - mangosolutions 6.15pm: Richard Saldanha - R in the ...

Read more »

Welsh test by permutations

November 1, 2009
By
Welsh test by permutations

WelshPerm <- function(response,variable,nperm=999,...){ base <- oneway.test(response~variable,...) base.p <- base$p.value base.W <- base$statistic count <- 1 # Permutation loop for(i in 1:nperm){ SAMPLE <- sample(response) we...

Read more »

R Tutorial Series: Summary and Descriptive Statistics

November 1, 2009
By
R Tutorial Series: Summary and Descriptive Statistics

Summary (or descriptive) statistics are the first figures used to represent nearly every dataset. They also form the foundation for much more complicated computations and analyses. Thus, in spite of being composed of simple methods, they are essential ...

Read more »