CODEWITHSUNDEEP
stringrsearchbioinformaticsdna-sequence
user2813606
user2813606

Reputation: 911

Need to count number of times sequence of letters occurs in string R

So I have a sequence of nucleotides and I need to count the number of times the word gaga appears in the sequence. This is what I have so far:

dna=c("a","g","c","t")
N=16
x=sample(dna,N,4)
x2=paste(x,collapse="")
x2

Here is an example output:

gtaggcctaattataa

Eventually, I am going to write a loop to make this run 100 times and plot a histogram of the counts of the word "gaga." So, my main question is: How can I write a function or code to search through the string x2 and count the number of occurrences of the word "gaga."

Any help would be appreciated! Thank you!

Upvotes: 1

Views: 2610

Answers (4)

Sven Hohenstein
Sven Hohenstein

Reputation: 81693

Here's an approach that counts overlaps too:

vec <- c("gagatttt",
"ttttgaga",
"gaga",
"tttgagattt",
"gagagaga",
"gagaga")


lengths(strsplit(vec, "ga(?=ga)", perl = TRUE)) - 1L
# [1] 1 1 1 1 3 2

Upvotes: 1

bartektartanus
bartektartanus

Reputation: 16080

Use stri_count_fixed from stringi package

    dna=c("a","g","c","t")
    N=160
    x=sample(dna,N,4)
    x2 <- stri_paste(x,collapse="")
    stri_count_fixed(x2,"gaga")
    ## 2

Upvotes: 1

Tyler Rinker
Tyler Rinker

Reputation: 109874

This is actually a wrapper for DWin's solution found in the qdap package:

x<- c("gtaggcctaattataa", "gtaggcctaatgagaataa", "gagagaga")

library(qdap)
qdap:::termco.h(x, "gaga", seq_along(x))

##   3 word.count term(gaga)
## 1 1          1          0
## 2 2          1          1
## 3 3          1          2

If you want just the counts:

qdap:::termco.h(x, "gaga", 1:3)[, 3]

Upvotes: 2

IRTFM
IRTFM

Reputation: 263362

?regex
sapply( gregexpr( "gaga", c("gtaggcctaattataa", 
                            "gtaggcctaatgagaataa", 
                            "gagagaga") ) ,
        function(x) if( x[1]==-1 ){ 0 }else{ length(x) } )
[1] 0 1 2

Upvotes: 4

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