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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,

Dear ?, I'm sure that there are many ways to do what you want; here's one: > cbind(concept_df, category= + ifelse(apply( + sapply(chemical_df$chemical, + function(x) grepl(x, concept_df$concept)), + 1, any), + "chemical", "")) concept category 1 butan

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:

I am encountering difficulty with NextMethod in 0.50-a4. We created a class of groupedData objects which are data.frames with additional attributes. The most important attribute is a formula describing roles of some of the variables in the experimental design. The class of such objects ends in "groupedData", "data.frame". The print method for the groupedData class simply

Dear mailing list, I'm stuck with a tricky problem here - at least it seems tricky to me, being not really talented in pattern matching and regex matters. I'm analysing amino acid mutations by position and type of mutation. E.g. (fictitious example) in position 92, I can find L92V, L92MV, L92I... L is in this example the wild-type amino-acid, and everything behind the position number is

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

I have two data frame. I want to use "chemical_df" to match "concept_df " concept_df <- data.frame(concept=c("butan acid ", "nano diamond particl", "slurri composit", "composit ph polis", " inorgan particl ", "grind liquid", "liquid formul", "nanoparticl", "size abras particl",

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

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

Package: xen Severity: wishlist I'm not maintaining xen anymore, so please remove me from uploaders. Cheers, -- System Information: Debian Release: squeeze/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores) Locale: LANG=C, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) Shell:

Author: acid Date: 2006-02-16 10:45:13 +0000 (Thu, 16 Feb 2006) New Revision: 3 Modified: trunk/changelog trunk/control Log: - Change maintainer and add uploaders field - Prepare changelog for new upload Modified: trunk/changelog =================================================================== --- trunk/changelog 2006-02-15 23:05:09 UTC (rev 2) +++ trunk/changelog 2006-02-16 10:45:13

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) >

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

test just testing please ignore... -- "I have learned that you should''nt compare yourself to others - they are more screwed up than you think." ...unknown "In the 60''s, people took acid to make the world weird. Now the world is weird and people take Prozac to make it normal." ..unknown _____________________________ Terry Remsik stripe-man.dyndns.org

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

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

... 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>

Ok, so I can use the structure-type to represent base or acid or salts. My next question is how union-typing works in LLVM. After reading a bit about, it's unclear to me if it is a "thing" anymore; my intuition -- and poking around in the sources is that it's a "no", it's been deprecated. Which then means that it doesn't much matter about typing LLVM. I can

I would like to fit a hierarchical regression model from Witte et al. (1994; see reference below). It's a logistic regression of a health outcome on quntities of food intake; the linear predictor has the form, X*beta + W*gamma, where X is a matrix of consumption of 82 foods (i.e., the rows of X represent people in the study, the columns represent different foods, and X_ij is the amount of

Hi, recently Ive installed Windows 2008 x64 HVM domain on Xen 4.0. On xen wiki is info: Support for Citrix WHQL-certified Windows PV drivers, included in XCP (Xen Cloud Platform). Xen Cloud Platform: So I installed them on Windows 2008 x64 domain and its not able to boot anymore: File: \windows\system32\Drivers\xevtchn.sys Status: 0xc0000428 Info: Windows cannot verify the digital