Question

我将FASTA格式的对齐方式导入R

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

我的对齐看起来像这样

Seq1 ATGCGGGAATGGACTCATGCATCG
Seq2 ATTCGATCTTGCTAGCTAGCTCGT
Seq3 ATATCGATGTCGATCGATCGACGA

如果我想在此对齐中调用单个序列（例如Seq2），我需要做什么？

Answer 1

我不知道read.dna()来自何处（有> 6000个CRAN包，以及近1000个Bioconductor个包）。您可以使用Biostrings包和

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

并做许多有用的事情，包括quick reference中描述的内容。如果最后你想要一个单一的字符向量，那么

as.character(dna[1])

或

as.character(dna[names(dna) == "Seq3"])

Answer 2

我猜你正在使用ape包。使用?read.dna

中的示例

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"

在将比对导入R后，如何检索单个DNA序列？

2 个答案: