[英]Get all possible permutations of a DNA sequence with an ambiguous base R
Lets say I have a DNA sequence with an ambiguous base, N
, where N can represent any base (its a flex position). 假设我有一个DNA序列,其碱基具有不明确的碱基N
,其中N可以代表任何碱基(它是一个柔性位置)。
dna.seq <- 'ATGCN'
I want a vector of every possible DNA sequence this could represent. 我想要一个可以代表的所有可能的DNA序列的载体。 It would look like: 它看起来像:
c('ATGCA','ATGCT','ATGCG','ATGCC')
The solution needs to account for dna sequences with multiple N
characters as well, which will create many more potential DNA sequences. 该解决方案还需要考虑具有多个N
字符的dna序列,这将产生更多潜在的DNA序列。
CJ
from data.table
can help you here: 来自data.table
CJ
在data.table
可以为您提供帮助:
library(data.table)
dna.seq <- 'ATGCN'
# split into components
l = tstrsplit(dna.seq, '', fixed = TRUE)
# replace N with all possibilities
all_bases = c('A', 'T', 'C', 'G')
l = lapply(l, function(x) if (x == 'N') all_bases else x)
# use CJ and reduce to strings:
Reduce(paste0, do.call(CJ, l))
# [1] "ATGCA" "ATGCC" "ATGCG" "ATGCT"
Flexibility to handle multiple N
: 灵活处理多个N
:
dna.seq <- 'ATNCN'
Reduce(paste0, do.call(CJ, l))
# [1] "ATACA" "ATACC" "ATACG" "ATACT" "ATCCA" "ATCCC" "ATCCG" "ATCCT"
# [9] "ATGCA" "ATGCC" "ATGCG" "ATGCT" "ATTCA" "ATTCC" "ATTCG" "ATTCT"
If you wanted to drop the data.table
dependency you could replace tstrsplit
with t(strsplit())
and CJ
with expand.grid
; 如果要删除data.table
依赖项,则可以将tstrsplit
替换为t(strsplit())
,将CJ
替换为expand.grid
; you'll just be sacrificing computational speed. 您只会牺牲计算速度。
dna.seq <- 'ATNGCN'
dna.seq.copy = dna.seq
while(grepl("N", dna.seq.copy[1])){
dna.seq.copy = as.vector(sapply(c("A", "C", "T", "G"), function(x) sub("N", x, dna.seq.copy)))
}
dna.seq.copy
# [1] "ATAGCA" "ATCGCA" "ATTGCA" "ATGGCA" "ATAGCC" "ATCGCC" "ATTGCC" "ATGGCC" "ATAGCT" "ATCGCT" "ATTGCT" "ATGGCT" "ATAGCG" "ATCGCG" "ATTGCG"
#[16] "ATGGCG"
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