Displaying 20 results from an estimated 300 matches similar to: "how to use writeFASTA in modality "append""
2009 Jul 17
0
How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...
I realize function write FASTA expects a list with two items, respectively, description and sequence.
However, just passing a list won't work (please, see code at the bottom of this message)
I saw there is the helper function CharacterToFASTArecords(x) that presumably generates the right input data format.
It would b very useful to get some example of CharacterToFASTArecords(x) usage.
The
2008 Aug 21
4
forgery Protection
Has anybody solved this issue. [
http://rubyforge.org/pipermail/facebooker-talk/2008-April/000552.html ] ?
NameError (undefined local variable or method `controller'' for
#<LeaveController:0xb7144abc>):
/app/controllers/application.rb:24:in `verify_authenticity_token''
2009 Apr 28
0
problems understanding error term in aov()
Hi all,
I'm having some trouble in understanding how to ste the Error() term in
the aov() function when fitting a hierarchical ANOVA.
I have data concerning the expression of 2 miRNAs in 3 different cell
lines, with 2 different extraction methods. The data is organized as
follows :
Line Extraction Target Expression
1 BC54 miRNA RNU48 22.48
2 BC54 miRNA
2011 Oct 10
3
Superposing mean line to xyplot
Dear R-users,
I'm using lattice package and function xyplot for the first time so
you will excuse me for my inexperience. I'm facing quite a simple
problem but I'm having troubles on how to solve it, I've read tons of
old mails in the archives and looked at some slides from?Deepayan
Sarkar but still can not get the point.
This is the context. I've got data on 9 microRNAs, each
2011 Jun 27
1
create a new data frame after comparing two columns of the previous data frame
Hi everyone,
I am trying to find a way to filter a table; If I am given for example the
following table:
> head(intra)
chr miRNA start end strand ACC hsa_ID
region region_start region_end gene_id transcrip_id
1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b";
exon 1102484 1102578 NR_029639 NR_029639
2 chr1
2011 May 31
2
correlatation matrix
Hi there,
I wonder if there is a way of efficiently generating a correlation matrix of two expression matrices. I want to correlate miRNA and mRNA expression and used the following code:
##dat.mi miRNA expression matrix, dat.m mRNA expression matrix
nc <- nrow(dat.mi)
cor.mat <- data.frame(rep(NA,nrow(dat.m)))
pval.mat <- data.frame(rep(NA,nrow(dat.m)))
for(i in 1:nc)
{
cr <- vector()
2018 Mar 21
1
Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository
Hi all!
While I am trying to read .cel files with oligo package:
afbatch=read.celfiles(list.celfiles())
I get an error:
Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository
How can I overcome this?
Thank you in advance
2011 Aug 05
1
CELT Test case failures
Hi ,
We've downloaded the CELTV0.11.1 source code from celt-codec.org . But
having trouble with mathops-test and tandem-test unit test that
exercises internal components of CELT codec, please find attached
document for each test case failure in details.
Also could you please give some inputs on CELT Low complexity code and
full version of the code, point me source code to CELT
2009 Jun 16
2
R and miRecords
I wonder whether R provides an interface to access miRecords data.
Particularly, I am looking for extracting humans miRNA and target genes sequences.
All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords)
I would greatly appreciate any suggestion even about other data bases from where it is possible to get the same sort of data.
I had a
2010 Feb 02
2
finding files whose name does NOT contain a given character
Unluckily I dela with miRNA files whose name may contain the character "*".
Because of the special meaning of "*" I have to remove it.
I found out how to make list.files() extract only those file names which contain a "*"
Namely:
# list.files(pattern="\\*")
Now I have to process all files whose name does NOT contain the character "*".
I cannot
2008 Nov 11
1
R: R: Hidden Markov Models
Thank you for your prompt answer.
The breathing signal observations are the amplitude values as a function of time and phase.
According to our model the hidden states are the different breathing types.
Subjects, whose respiratiion process is regular, are likely to breathe, keeping the same cycle pattern/type,
for many consecutive cycles. therefore dwelling in the same hidden state.
The more
2000 Jul 14
1
Compiling question about the nightly CVS download
I'm doing something wrong but the directions I follow seem simple:
tar xvfz vorbis-nightly-cvs.tgz (in /root)
cd vorbis
./configure
make
make install
There didn't seem to be any unusual output from configure or make,
but make install results in:
cat install.sh >install
chmod a+x install
both of these files are empty.
The directories /usr/local/bin, usr/local/man and
2004 Mar 28
1
add "select" to subset docs (PR#6710)
Full_Name: ivo welch
Version: current
OS: linux
Submission from: (NULL) (130.132.33.212)
* In the ?subset page, please add
subset( dataframe, select= c(-column1,-column2) )
returns a dara frame that is without columns 1 and 2 .
* Also, in ?lm, it would be nice to add a few more words about how to get a
residuals vector of the same length as the variable vectors, even if there
2009 Oct 19
1
updating columns using other column as reference
Dear R-gurus,
Just supose I have a dara.frame that looks like
myDF<-read.table(stdin(),head=T,sep=",")
codID,namesp,k1,k2,k3,k4
1,spA,2,5,6,3
2,spB,4,5,4,6
3,spC,2,1,5,6
4,spC,5,4,3,2
5,spD,1,2,3,4
6,spE,2,4,3,1
I need to update the columns k1-k4 with the namesp, but
considering the math between Kx and codID.
My desired output must looks like:
codID,namesp,k1,k2,k3,k4
2003 Jul 17
0
Silverman modality test
Dear R users,
I've written the following functions to implement Silverman's modality
test ("Using kernel density estimates to investigate multimodality", J.R.
Stat. Soc. B, 43, (1981), 97-99.), and I tested them on the Chondrite data
set (Good & Gaskins, J. Amer. Stat. Ass., 75, (1980), 42-56). Values for
the critical window width seem OK, which is not the case for the
2008 Dec 02
1
help with package Rwave
I am looking for some explanations about the usage of the poorely documented R paclkage Rwave.
Has anyone ever tried out its functions for Wavelet Analysis ?
Thank you so much.
Maura
Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM!
Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer
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2008 Dec 09
1
package "wmtsa": wavCWTPeaks error
I keep getting the following error when I look for minima in the series:
> aa.peak <- wavCWTPeaks (aa.tree)
Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "0")) :
invalid 'row.names' length
How can I work it around ?
Thank you.
Regards,
Maura
Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM!
2008 Dec 12
1
Eror handling with R
Is there any way to handle errors retuened by R functions ... something like the exception handling in C++ ?
Thank you so much,
Maura
Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM!
Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer
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2000 Oct 13
3
Current hardware requirements for decoding? (skipping problem)
The vorbis FAQ mentions that decoding vorbis should use roughly the same
resources as decoding MP3's, but that the current source is not optimized. So
what is the current requirement? I have a Pentium 133 with 64 megs and I
cannot get .ogg files to play without skipping. I've tried encoding .wav
files and downloading .ogg files from www.vorbis.com and playing them on
Winamp with
2002 Jul 25
3
Is there an oggenc low bit rate HOWTO?
First let me say that I was absolutely astounded at the sound quality
when using oggenc at q = -1 (around 50 kbps). So much so, that I'm
anxious to try some of the lower bit rates that were mentioned in the
announcement for 1.0:
... audio and music at fixed and variable bitrates from 16 to 128
kbps/channel.
But I am having trouble finding how to use either oggdrop or oggenc to
get these