search for: s2c

Hi, Try: vec1<- "mue#d/sjbijk at ruepvnvbnceiicrpgxkgcyl@keduhqvqi/ubudvxopddpfddgitrynzshzdcwgneyffrkpbxwilwqngrsals#geqmtkcpkp/qecgdfa#uag" library(seqinr) ?res<-lapply(0:4,function(i) lapply(2:5,function(j) splitseq(s2c(gsub("[#@/]","",vec1)),word=j,frame=i))) #or library(stringr) res1<-lapply(0:4,function(i) lapply(2:5,function(j) splitseq(s2c(str_replace_all(vec1,"[[:punct:]]","")),word=j,frame=i))) #or res2<-lapply(0:4,function(i) lapply(2:5,function(j) splitseq(s2c...

Hiya, I am trying to look at the similarities between a number of sequences, for example i am trying to see how similar "ababbbassdaa" is to "addffggssbbsbbs" I was wondering is the some way for me to see how similar they are in terms of, for example, number of a's, number of b's, how often a and ab are consecutive, how often abab is together etc. Any advice

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd [[alternative HTML version deleted]]

...ge amounts of data. I assume it's because I don't know how to avoid using loops. Logical subscripts are more desirable, but I don't know how to implement them. One example of that issue: library(seqinr) GCsequence <- vector() for( i in 1:(length(data$sequence))) { c(GCsequence,GC(s2c(data$sequence[i])))->data$GCsequence[i] } rm(GCsequence) How should I speed up that? Thank you, Retama -- View this message in context: http://www.nabble.com/Loop-avoidance-and-logical-subscripts-tp23652935p23652935.html Sent from the R help mailing list archive at Nabble.com.

I need to increment cells of a matrix (collusionM). The indexes to increment are in an index (matchIndex). This is some of the code for (j in 1:(rows-1)) matchIndex[[j]] <- which(mx[j]==mx) for (j in 1:(rows-1)) collisionM[j,matchIndex[[j]]] <- collisionM[j,matchIndex[[j]]] + 1 I could put them in the same loop but this is slower. The first for statement is fine. It finds the matches

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

Hello, I have a big number lets say of around hundred digits. I want to subset that big number into consecutive number of 5 digits and find the product of those 5 digits. For example my first 5 digit number would be 73167. I need to check the product of the individual numbers in 73167 and so on. The sample number is as follows:

...K-ry+kt z!z$j5xW*0HN0~3)binCr7vXMc6>?C!et)4y9twTjL^$!lrm24ss_7<c<KSy3f9&L9 zE-)87-r&)xd^-JTHV(g-!mIve->rHE?mR+Z7k7i}iMTUFbk0jcqp$Ox5SzcS)y=XW zy`I6r#vOCe$C9fnBOB3b`<h8NQIMP`YMfs%fUs-RJ|keeOA!B2I1WKXKbh#6rBLGv zgx5BW7qd2t(K%849T_ggkVP!&;5Rj?T1%8`v=o4uH}3a at dDeA1tMV770>s2C$U8JF z!ggf*8&%zv)Z}t6U9iOtDyE8l(<nfcx8+b?MsE|wtL0cEr*zb;Q87 at SzBo@TnJ2+Y z%Eu3CUW<{20KinW3;p4McE`NzjTV{jEIIt2OLMZYFqnM74xm$=$C_5GYiT1Y8x3!w z5SQl3s5Tp+v|N&H_xF?E#fmA{PbOixW!HB;-JknB4HJjte1%gN78{qoteaA&B!AFI zN7NmDudq7y33A5li6DG_&I4R63 at HDacjkLvL(vRrO2k}hAwx7Z)FWf31d4M8R)iL...