在将比对导入R之后，如何检索单个DNA序列？

我将FASTA格式的对齐方式导入到R中

    read.dna(file.choose(),format="fasta",skip=0)

我的路线看起来像这样

Seq1 ATGCGGGAATGGACTCATGCATCG
Seq2 ATTCGATCTTGCTAGCTAGCTCGT
Seq3 ATATCGATGTCGATCGATCGACGA

---

如果我想从这个序列中调用单个序列（例如Seq2），我需要做什么？

我不知道

read.dna（）

从哪里来（有超过6000个CRAN包，将近1000个包）。你可以用这个包和

library(Biostrings)
dna = readDNAStringSet("path/to.fasta")

并做许多有用的事情，包括。如果最后需要一个字符向量，那么

as.character(dna[1])

或

---

我猜您正在使用

ape

包。使用

？read.dna

library(ape)
cat(">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
">No304",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
">No306",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
file = "exdna.txt", sep = "\n")
ex.dna4 <- read.dna("exdna.txt", format = "fasta")

ex.dna4[dimnames(ex.dna4)[[1]]=='No304',]
#1 DNA sequences in binary format stored in a matrix.

#All sequences of same length: 40 

#Labels: No304 

#Base composition:
#    a     c     g     t 
#0.475 0.300 0.025 0.200 

as.character(ex.dna4[dimnames(ex.dna4)[[1]]=='No304'])
#[1] "a" "t" "t" "c" "g" "a" "a" "a" "a" "a" "c" "a" "c" "a" "c" "c" "c" "a" "c"
#[20] "t" "a" "c" "t" "a" "a" "a" "a" "a" "t" "t" "a" "t" "c" "a" "a" "c" "c" "a"
#[39] "c" "t"

库（ape）
猫（“>No305”，
“NTTCGAAAACACACACTACTAAANTTATACAGTCACT”，
“>No304”，
“attcgaaaacacacctactaaaattacacact”，
“>No306”，
“ATTCGAAAAAACACTACTAAAATTATCATCAT”，
file=“exdna.txt”，sep=“\n”）
ex.dna4
library(ape)
cat(">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
">No304",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
">No306",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAATCACT",
file = "exdna.txt", sep = "\n")
ex.dna4 <- read.dna("exdna.txt", format = "fasta")

ex.dna4[dimnames(ex.dna4)[[1]]=='No304',]
#1 DNA sequences in binary format stored in a matrix.

#All sequences of same length: 40 

#Labels: No304 

#Base composition:
#    a     c     g     t 
#0.475 0.300 0.025 0.200 

as.character(ex.dna4[dimnames(ex.dna4)[[1]]=='No304'])
#[1] "a" "t" "t" "c" "g" "a" "a" "a" "a" "a" "c" "a" "c" "a" "c" "c" "c" "a" "c"
#[20] "t" "a" "c" "t" "a" "a" "a" "a" "a" "t" "t" "a" "t" "c" "a" "a" "c" "c" "a"
#[39] "c" "t"