An R Introduction to Statistics | R Tutorial.
Index of /doc/contrib. Index of /~serafim/CS262_2008/notes. Package HMM. Hidden Markov Model for CpG islands — Stats366 / Stats 166 Course Notes. Does a Short DNA Stretch Come from a CpG Island? Here we use likelihood scores as discriminatory statistic. We need to model both the CpG Islands and the regions that are not CpG Islands. For this we need training sequences. We can collect databases of nucleotides from both types of sequences. * Collect a database of 60,000 nucleotides * Extract 48 putative CpG Islands * For the putative CpG Regions compute the transition probabilities from nucleotide s to nucleotide t using a Markovian Model a^+_{s,t} = \frac{c^+_{s,t} }{ \sum_k c^+_{s,k}} c^+_{s,t} is the number of times that s is followed by t in the database of CpG Islands. * Similarly for the regions without CpG Islands a^-_{st}= \frac{c^-_{s,t}}{\sum_k c^-_{s,k}} * Construct table of transition probabilities Table of Transition Probabilities for CpG Islands Table of Transition Probabilities for non CpG Islands Calculate the Log-Odds ratio for a sequence x: Scores S(x) allow discrimination of a model (+) against another (-) Score Computation.
Hidden Markov Models — Bioinformatics 0.1 documentation. A little more about R In previous practicals, you learnt how to create different types of variables in R such as scalars, vectors and lists. Sometimes it is useful to create a variable before you actually need to store any data in the variable. To create a vector without actually storing any data in it, you can use the numeric() command to create a vector for storing numbers, or the character() command to create a vector for storing characters (eg. “A”, “hello”, etc.) For example, you may want to create a vector variable for storing the square of a number, and then store numbers in its elements afterwards: > myvector <- numeric() # Create a vector "myvector" for storing numbers > for (i in 1:10) { myvector[i] <- i*i } # Fill in the values in the vector "myvector" > myvector # Print out the vector "myvector" [1] 1 4 9 16 25 36 49 64 81 100 Note that if you try to store numbers in the elements of a vector that you have not yet created, you will get an error message, for example:
Welcome to a Little Book of R for Bioinformatics! — Bioinformatics 0.1 documentation. Welcome to a Little Book of R for Bioinformatics! — Bioinformatics 0.1 documentation. Index of /jornadasbioestadistica2011/doc/CursoCasella. Introduction to R and Bioconductor. Introduction to R and Bioconductor Seattle, USA Instructors Chao-Jen Wong Herve Pages Marc Carlson Martin Morgan Nishant Gopalakrishnan Patrick Aboyoun Seth Falcon Description This course introduces R and Bioconductor tools for analysis of high-throughput microarray and short read sequence data. It is designed for beginning or intermediate users of R and Bioconductor. A major theme for this workshop is reproducible research. Materials Contact us: webmaster@bioconductor.org Hosting provided by Fred Hutchinson Cancer Research Center Copyright © 2003 - 2014 Search:
Teach. Manuals. UseR-SC-10-B.dvi - UseR-SC-10-B-Part1.pdf.