在 R 中使用 seqinr package 计算 DNA 序列的碱基

Question

I have an array which was extracted from a fasta file

> dat
  [1] "t" "a" "t" "t" "t" "a" "c" "c" "g" "a" "c" "g" "a" "a" "a" "t" "t" "a" "a" "t" "a" "c" "c" "a" "t" "c" "a" "g" "g" "g" "t" "a" "t"
  [34] "t" "a" "a" "g" "a" "t" "g" "c" "t" "a" "c" "c" "a" "a" "c" "g" "t" "g" "g" "t" "a" "t" "t" "a" "a" "a" "a" "t" "g" "t" "g" "c" "c"
  [67] "c" "a" "a" "c" "c" "g" "c" "g" "a" "a" "a" "a" "a" "g" "a" "a" "a" "g" "t" "g" "g" "t" "a" "t" "a" "t" "a" "g" "g" "a" "a" "a" "a"

The sequence is much longer but for that is unimportant I wish to break up the first 100000 characters in this array into intervals of length 1000 and count the number of "g" bases in each interval. So far I've tried:

library(seqinr)
intervals = 1000*(0:99)
g_count = count(dat[intervals+1:intervals+1000], 1)[["g"]]

but this returns the error: numerical expression has 100 elements: only the first used any help is appreciated

Answer 1

To count number of 'g' in each interval you could use this base R approach:

n <- 1000
result <- tapply(dat, ceiling(seq_along(dat)/n), function(x) sum(x == 'g'))

For example, for this vector of length 33 we divide data into interval of 11.

dat <- c("t", "a", "t", "t", "t", "a", "c", "c", "g", "a", "c", "g", 
"a", "a", "a", "t", "t", "a", "a", "t", "a", "c", "c", "a", "t", 
"c", "a", "g", "g", "g", "t", "a", "t")

n <- 11
result <- tapply(dat, ceiling(seq_along(dat)/n), function(x) sum(x == 'g'))
result

#1 2 3 
#1 1 3 

Answer 2

We can use rowsum with gl in base R

rowsum(+(dat == 'g'), as.integer(gl(length(dat), n, length(dat))))

data

dat <- c("t", "a", "t", "t", "t", "a", "c", "c", "g", "a", "c", "g", 
"a", "a", "a", "t", "t", "a", "a", "t", "a", "c", "c", "a", "t", 
"c", "a", "g", "g", "g", "t", "a", "t")

n <- 11