Displaying 20 results from an estimated 3000 matches similar to: "Pattern Matching within Vector?"
2010 Jan 17
6
More than on loop??
hello every one,
How to function more than one loop in R? I have the following problem to be
solved with the a method of three loops, can you help me please?
The data is attached with this message.
The data is composed of two parts, cleaved (denoted by ?cleaved?) and non
cleaved (denoted by ?noncleaved?).
? to access to the ith peptide, you can use X$Peptide[i]
? to access to the ith label,
2005 Jan 06
1
Calculating a table of symbol frequencies
Hello all:
I have a protein sequence alignment in a data frame (align1, 72 x 236),
where each row is a protein and each column a site in the alignment. AA is
vector of amino acid symbols plus "-" (gap). I can calculate amino acid
frequencies at each site by:
>align1.F <- matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236)))
>for(i in 1:236)
>
2018 May 03
0
Package for Molecular Properties
library(sos)
(mp <- findFn('{molecular properties}'))
????? ** found 7 matches in 4 packages and opened two web pages in my
default browser with (a) the 7 matches and (b) the 4 packages. The first
function was something for amino acids, like you suggested.? Two others
returned compound and substance information from PubChem.
????? Does this help?
????? Spencer
On
2018 May 03
3
Package for Molecular Properties
All
Is there a package or library that will, given a nucleotide sequence
1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law)
2. calculate molecular weight
3. return it's complementary sequence
I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids.
Any pointers, etc. would be
2010 Jan 02
4
caculate the frequencies of the Amino Acids
may some one please help me to sort this out, i am trying to writ a R code
for calculating the frequencies of the amino acids in 9 different sequences,
i want the code to read the sequence from external text file, i used the
following code to do so:
x<-read.table("sequence.txt",header=FALSE)
then i defined an array for 20 amino acids as following:
2012 Jul 23
3
How to do the same thing for all levels of a column?
Dear all,
I am a R beginner, and I am looking for a way to do the same thing for all
levels of a column in a table.
Basically, I have a bunch of protein sequences composed of different amino
acid residues, and each residue is represented by an uppercase letter. I
want to calculate the ratio of different amino acid residues at each
position of the proteins. Here is an example table:
Proteins
2018 May 03
1
Package for Molecular Properties
... In addition, you may wish to also post on the Bioconductor list
for this sort of thing.
-- Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Thu, May 3, 2018 at 12:58 AM, Spencer Graves
<spencer.graves at effectivedefense.org>
2005 Jan 03
1
Calculating symbol (letter) frequencies
Hello:
I am attempting to use R to analyze amino acid frequencies in aligned
protein sequences and need some help. So far, I have imported my sequence
alignment into a data frame (lets call it "alignment") with each site in one
column, so that I have a data frame consisting of columns of letters (the 21
amino acid symbols plus "-") with row names being the corresponding
2006 Jun 18
2
analyze amino acid sequence (composition)of proteins
Dear R-helpers:
thank your for your attention.
i am a newer to R and i am doing some protein category classification based on
the amino acid sequence.while i have some questions urgently.
1. any packages for analysis amino acid sequence
2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB"
3. based on "AAABBB",how can i get some
2006 Jun 18
1
about the analysis of strings, thanks
Dear R-helpers:
thank your for your attention.
i am a newer to R and i am doing some protein category classification based on
the amino acid sequence.while i have some question urgent.
1. any packages for analysis amino acid sequence
2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB"
3. based on "AAABBB",how can i get some
2017 Aug 04
1
legend and values do not match in ggplot
I have following codes for ggplots. The legends are given in the plot do
not match with the values specified in the codes given below. Your helps
highly appreciated.
Greg
library(ggplot2)
p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+
theme_bw() +theme(panel.border=element_blank()) +
geom_point(size=3)
p2<-p+scale_color_manual(name="Super.Pathway",
2013 Nov 01
1
Package(s) for making waffle plot-like figures?
Dear all,
I am trying to make a series of waffle plot-like figures for my data to
visualize the ratios of amino acid residues at each position. For each one
of 37 positions, there may be one to four different amino acid residues. So
the data consist of the positions, what residues are there, and the ratios
of residues. The ratios of residues at a position add up to 100, or close
to 100 (more on
2008 Jan 17
4
aaMI
hi
i am new to R language. I want to use aaMI package which calculates the
amino acid mutual interaction for a given protein sequence. I had installed
the package but when i run the program it gives me the error could not find
function "aaMI". can anyone tell me what might be the problem..
--
View this message in context: http://www.nabble.com/aaMI-tp14915744p14915744.html
Sent from
2017 Jan 05
2
LLVM-based Mutation Testing, first results.
Hello, everybody.
We are working on a tool for mutation testing. The work is still in progress and far away from being done.
However, we have got some results already. And we would like to share them with you.
But, let me give you a brief introduction first.
### Mutation Testing
In a nutshell, Mutation Testing is a way to evaluate a quality of a test suite.
The approach suggests introducing a
2011 Jul 15
6
how to order each element according to alphabet
Hi there,
I have a large amino acid csv file like this:
input.txt:
P,LV,Q,Z
P,VL,Q,Z
P,ML,QL,Z
There is a problem with this file, since LV and VL are in fact the same
thing.
How do I order each element according to alphabetical order so that the
desired output would look like:
output.txt:
P,LV,Q,Z
P,LV,Q,Z
P,LM,LQ,Z
--
View this message in context:
2011 Mar 22
1
Best HMM package to generate random (protein) sequences?
Dear All,
I would like to generate random protein sequences using a HMM model.
Has anybody done that before, or would you have any idea which package
is likely to be best for that?
The important facts are that the HMM will be fitted on ~3 million
sequential observations, with 20 different states (one for each amino
acid). I guess that 2-5 hidden states should be enough, and an order
of 3 would
2007 Jun 12
3
Appropriate regression model for categorical variables
Dear users,
In my psychometric test i have applied logistic regression on my data. My
data consists of 50 predictors (22 continuous and 28 categorical) plus a
binary response.
Using glm(), stepAIC() i didn't get satisfactory result as misclassification
rate is too high. I think categorical variables are responsible for this
debacle. Some of them have more than 6 level (one has 10 level).
2005 Feb 16
0
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2009 Oct 01
3
[LLVMdev] PHI and Allocas
Hi,
I'm incrementing my toy compiler to account for variable mutations
around if/else blocks.
Reading the Kaleidoscope tutorial, I've learnt that I can substitute
the PHI node creation by allocas and retrieving the value later, if
needed. The Kaleidoscope example seems to account for one value only,
the result of:
Value *ThenV = Then->Codegen();
(...)
Value *ElseV =
2017 Jul 03
3
reshaping the data
Dear all,
I would appreciate please a piece of help regarding the use of acast/dcast
functions in reshape2 package.
Specifically, I'm working with a data frame, that has information about
SAMPLE, GENE, and TYPE of MUTATION (as shown below):
Sample Gene Type
22M AEBP1 SNV
17M AEBP1 SNV
22M ATR INDEL
22M ATR SNV
11M BTK SNV
11M BTK