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matchPWM is now part of Biostrings 2.7.47 in…

matchPWM() is now part of Biostrings 2.7.47 (in BioC devel, so you need R-2.7).

Load Biostrings:

   library(Biostrings)

Suppose 'pwm' contains a Position Weight Matrix, let's say:

   pwm <- rbind(A=c( 1,  0, 19, 20, 18,  1, 20,  7),
                C=c( 1,  0,  1,  0,  1, 18,  0,  2),
                G=c(17,  0,  0,  0,  1,  0,  0,  3),
                T=c( 1, 20,  0,  0,  0,  1,  0,  8))

Note that this is just a standard integer matrix with the 4 DNA base letters
as row names (having these row names is mandatory).
Some low-level utility functions are available for manipulating this kind of
matrix:

   > maxWeights(pwm)  # the max weight in each column
   [1] 17 20 19 20 18 18 20  8

   > maxScore(pwm)  # the max possible score
   [1] 140

Let's match 'pwm' against Human chr1:

   library(BSgenome.Hsapiens.UCSC.hg18)
   chr1 <- Hsapiens$chr1

Number of "best" matches:

   > countPWM(pwm, chr1, min.score="100%")  # takes about 5 seconds on my system
   [1] 5152

With a lower cut-off value:

   m <- matchPWM(pwm, chr1, min.score="90%")

See the 10 first matches ("first" means "smallest chromosome location", NOT "best"
matches):

   > m[1:10]
     Views on a 247249719-letter DNAString subject
   subject: TAACCCTAACCCTAACCCTAACCCTAACCCTAAC...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
   views:
        start   end width
    [1] 31931 31938     8 [GTAAACAA]
    [2] 33324 33331     8 [GTAAACAT]
    [3] 38425 38432     8 [GTAAACAG]
    [4] 39177 39184     8 [GTAAACAC]
    [5] 46971 46978     8 [GTAAACAT]
    [6] 49952 49959     8 [GTAAACAT]
    [7] 70381 70388     8 [GTAAACAG]
    [8] 74359 74366     8 [GTAAACAC]
    [9] 90714 90721     8 [GTAAACAT]
   [10] 96544 96551     8 [GTAAACAC]

The speed could be improved, maybe by a factor 2 (or more, for longest PWMs).

Also maybe an additional argument could be added to let the user control how
the returned matches should be sorted ("left-to-right" or "best-first")?

Unlike MatInspector or the transfac-tool, there is no facility yet to suggest
individual cut-off values depending on the length of the PWMs.

See '?matchPWM' for more information (e.g. how to search the minus strand of
the chromosome).

https://stat.ethz.ch/pipermail/bioconductor/2008-April/022029.html

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Save R function to a text file latex…

Save R function to a text file

latex.code <- function(){
   cat("\\begin{align}\n")
   cat("[X'X]^{-1}X'y\n")
   cat("\\end{align}\n")
}
sink(file='ols.txt')
latex.code()
sink()

http://stackoverflow.com/questions/6222565/how-can-i-save-text-to-a-file-in-r

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Sumatra is a tool for managing and tracking…

Sumatra is a tool for managing and tracking projects based on numerical simulation and/or analysis, with the aim of supporting reproducible research. It can be thought of as an automated electronic lab notebook for computational projects.

It consists of:

a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the experiment, annotating these records, linking to data files, etc.
a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results.
a Python API, on which smt and smtweb are based, that can be used in your own scripts in place of using smt, or could be integrated into a GUI-based application.
Sumatra is currently alpha code, and should be used with caution and frequent backups of your records.

http://packages.python.org/Sumatra/index.html

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Installing Python without root http stackoverflow com questions…

Installing Python without root.

http://stackoverflow.com/questions/622744/unable-to-install-python-without-sudo-access

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Quick and easy submission of R on Sun…

Quick and easy submission of R on Sun Grid Engine

Easiest way to submit R jobs

Here are two scripts and a symlink I created to make it easy as possible to submit R jobs to your Grid:

qsub-R

If you normally do something along the lines of:

user@exec:~$ nohup nice R CMD BATCH toodles.R
Now all you need to do is:

user@submit:~$ qsub-R toodles.R
Your job 3540 (“toodles.R”) has been submitted
qsub-R is linked to submit-R, a script I wrote. It calls qsub and submits a simple shell wrapper with the R file as an argument. It ends up in the queue and eventually your output arrives in the current directory: toodles.R.o3540

Download it and install it. You’ll need to make the ‘qsub-R’ symlink to ‘3rd_party/uoa-dos/submit-R’ yourself, although there is one in the package already for lx24-x86: qsub-R.tar (10 KiB, tar)

http://www.stat.auckland.ac.nz/~kimihia/sun-grid#submitting

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When Mendeley bibliography duplicates instead of refreshing Check…

When Mendeley bibliography duplicates instead of refreshing.

Check whether the following option is set in Word 2007:
Office button->Word Options->Advanced->General->Confirm file format conversion on open

http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/1384943-bug-refresh-bibliography-in-word-creates-duplicat

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Remove the first line in Perl $first line…

Remove the first line in Perl

$first_line = <>;

while (<>) {
    do_something();
}