Publications by R on Guangchuang Yu
highlight R syntax in wordpress using wp-codebox
Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in WordPress. I found that WP-CodeBox use GeShi for syntax highlighting as WP-Syntax does.I used this plugin when I posted per...
1383 sym
ClusterProfiles
It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a variety of gene clusters may gi...
2315 sym R (2199 sym/3 pcs) 2 img 1 tbl
The S3 OOP system
R currently supports two internal OOP systems (S3 and S4), and several others as add-on packages, such as R.oo, and OOP. S3 is easy to use but not reliable enough for large software projects. The emphasis of the S3 system was on generic functions and polymorphism. It’s a function centric system which is different to class centric system like JA...
2644 sym R (606 sym/7 pcs)
Listing gene IDs from hyperGTest
hyperGTest compute Hypergeomtric p-values for over or under-representation of each GO term in the specified category among the specified gene set. *geneSample* was used as an example. > geneSample [1] "3987" "11167" "8683" "23576" "80173" "857" "64960" "3178" "93099" "100302736" "3916" "8663" "3...
1792 sym R (853 sym/3 pcs)
upgrade R – F77 cause compilation error
I try to compile the source code of R 2.12 on CentOS, but it throw an error when trying to install *cluster*. * installing *source* package ‘cluster’ ... ** libs gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -fpic -g -O2 -c clara.c -o clara.o g77 -fpic -g -O2 -c daisy.f -o daisy.o g77 -fpic -g -O2 -c dysta.f -o dy...
1834 sym R (3576 sym/4 pcs)
GOSemSim redesign in terms of S4 classes
I started to develop GOSemSim package two years ago when I was not quite familiar with R. I am very happy to see that someone use it and found it helpful. I try to learn S4 and redesign GOSemSim with S4 classes and methods in the pass two weeks, and the very first version was implemented. As I’m not very familiar with S4, the package may need ...
1369 sym R (2012 sym/2 pcs)
The avalanche of publications mentioning GO
Gene Ontology is the de facto standard for annotation of gene products. It has been widely used in biological data mining, and I believe it will play more central role in the future. Publications mentioning GO was collected and deposited in GO ftp, and can be accessed (ftp://ftp.geneontology.org/go/doc/). I count the number of publicans by year, ...
1408 sym R (218 sym/1 pcs) 2 img
bubble chart by using ggplot2
The visualization represented by Hans Rosling’s TED talk was very impressive. FlowingData provides a tutorial on making bubble chart in R. I prefer ggplot2 for graphics. crime <- read.csv("http://datasets.flowingdata.com/crimeRatesByState2008.csv", header=TRUE, sep="\t") p <- ggplot(crime, aes(murder,burglary,size=population, label=state)) p...
1122 sym R (320 sym/1 pcs) 2 img
Root finding
Numerical root finding methods use iteration, producing a sequence of numbers that hopefully converge towards a limits which is a root. In this post, only focus four basic algorithm on root finding, and covers bisection method, fixed point method, Newton-Raphson method, and secant method. The simplest root finding algorithms is the bisection meth...
2466 sym R (878 sym/4 pcs)
Project Euler — Problem 187
http://projecteuler.net/index.php?section=problems&id=187 A composite is a number containing at least two prime factors. For example, 15 = 3 × 5; 9 = 3 × 3; 12 = 2 × 2 × 3. There are ten composites below thirty containing precisely two, not necessarily distinct, prime factors: 4, 6, 9, 10, 14, 15, 21, 22, 25, 26. How many composite integers, ...
1428 sym R (312 sym/1 pcs)