はbiostringパッケージに

Question

みましょう例えば、私は3列

myseq=DNAStringSet(c("ATGACGAACTGTAAAGGACTGCACGGCC", 
        "TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG", 
        "GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT")) 

を持っていると私は検索する必要があるパターンは、私が情報をコンパイルしたい

fragments= DNAStringSet(c("ACTG","AAAA")) 

counts=vcountPDict(fragments,myseq) 

です異なる列のフラグメントの見出しDNA seq、fragment、およびcountを持つ表の形式。したがって、それをうまく提示できます。

Answer 1

library(Biostrings) 
myseq = DNAStringSet(c(
    "ATGACGAACTGTAAAGGACTGCACGGCC", 
    "TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG", 
    "GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT" 
)) 

fragments = DNAStringSet(c("ACTG","AAAA")) 
counts = vcountPDict(fragments, myseq) 

# then use command of expand.grid and name two of the columns 
a = expand.grid(seqID = myseq, pattern = fragments) 

# Another variable to account for the frequency of each pattern 
b = expand.grid(freq = counts) 
r = cbind.data.frame(a, b) 

結果は、おそらく検索用語をループに `sapply`または` lapply`を使用

> r 
             seqID pattern freq 
1    ATGACGAACTGTAAAGGACTGCACGGCC ACTG 2 
2 TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG ACTG 0 
3 GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT ACTG 1 
4    ATGACGAACTGTAAAGGACTGCACGGCC AAAA 2 
5 TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG AAAA 1 
6 GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT AAAA 0 

Answer 2

は、私はちょうどあなたが行くと

seq.counts <- colSums(sequence[,2:3]) 
seq.means <- colMeans(sequence[,2:3]) 

をするか、またはあなたが行うことができ、このここHow to take a word and create an indicator variable based on the word's presence in comments?

fragment <- c("ACTG","AAAA") 
sequence <- c("ATGACGAACTGTAAAGGACTGCACGGCC", 
       "TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG", 
       "GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT") 

sequence <- data.frame(sequence, sapply(fragment, function(i) as.numeric(grepl(i, sequence))))  
sequence 
             sequence ACTG AAAA 
1    ATGACGAACTGTAAAGGACTGCACGGCC 1 0 
2 TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG 1 1 
3 GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT 1 0 

ここからのような質問をし

になり

sequence <- data.frame(sequence, sapply(fragment, function(i) str_count(sequence, i))) 

> sequence 
            sequence ACTG AAAA 
1    ATGACGAACTGTAAAGGACTGCACGGCC 2 0 
2 TCCAACGAGAAAACCTGTGGGCACGGCCAAAACTGTTGGG 1 2 
3 GGCGGGGACAAATGTTCCATGACTGGCCTTTAAAGGCCTAGAT 1 0 

colSumsまたはcolMeansを使用できます。