将字符串数据集转换为矩阵答案

【问题标题】：Convert string dataset to a matrix将字符串数据集转换为矩阵
【发布时间】：2017-04-02 08:39:31
【问题描述】：

我有一个由制表符分隔的数据集，所以我想将以下数据集转换为矩阵

CATGGGGAAAACTGA
CCTCTCGATCACCGA
CCTATAGATCACCGA
CCGATTGATCACCGA
CCTTGTGCAGACCGA

我以前用过

rbind(strsplit("CATGGGGAAAACTGA","")[[1]],
        strsplit("CCTCTCGATCACCGA","")[[1]],
        strsplit("CCTCTCGATCACCGA","")[[1]],
        strsplit("CCTATAGATCACCGA","")[[1]],
        strsplit("CCGATTGATCACCGA","")[[1]],
        strsplit("CCTTGTGCAGACCGA","")[[1]])

这会产生：

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
[1,] "C"  "A"  "T"  "G"  "G"  "G"  "G"  "A"  "A"  "A"   "A"   "C"   "T"   "G"   "A"  
[2,] "C"  "C"  "T"  "C"  "T"  "C"  "G"  "A"  "T"  "C"   "A"   "C"   "C"   "G"   "A"  
[3,] "C"  "C"  "T"  "C"  "T"  "C"  "G"  "A"  "T"  "C"   "A"   "C"   "C"   "G"   "A"  
[4,] "C"  "C"  "T"  "A"  "T"  "A"  "G"  "A"  "T"  "C"   "A"   "C"   "C"   "G"   "A"  
[5,] "C"  "C"  "G"  "A"  "T"  "T"  "G"  "A"  "T"  "C"   "A"   "C"   "C"   "G"   "A"  
[6,] "C"  "C"  "T"  "T"  "G"  "T"  "G"  "C"  "A"  "G"   "A"   "C"   "C"   "G"   "A"

但是当数据集非常大时，这个过程很累人。我怎么能自动完成呢？

【问题讨论】：

使用do.call：类似于do.call("rbind", lapply(myDNAVec, strsplit, split=""))。
序列长度是否固定，始终为 15？
@lmo 不需要lapply。 strsplit(myDNAvec, split = '') 会起作用。
可能相关问答：Faster way to read fixed-width files in R
@KonradRudolph 谢谢。 lapply 创建了一个不必要的嵌套，并且可能会产生额外的开销。 do.call(rbind, strsplit(myDNAvec, split = '')) 更好。

标签： r string split bioinformatics

【解决方案1】：

您可以使用read.fwf 分割成单个字符：

read.fwf(textConnection("CATGGGGAAAACTGA
CCTCTCGATCACCGA
CCTATAGATCACCGA
CCGATTGATCACCGA
CCTTGTGCAGACCGA"), rep(1, nchar("CATGGGGAAAACTGA")))
#  V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15
#1  C  A  T  G  G  G  G  A  A   A   A   C   T   G   A
#2  C  C  T  C  T  C  G  A  T   C   A   C   C   G   A
#3  C  C  T  A  T  A  G  A  T   C   A   C   C   G   A
#4  C  C  G  A  T  T  G  A  T   C   A   C   C   G   A
#5  C  C  T  T  G  T  G  C  A   G   A   C   C   G   A

您可能希望传递文件名而不是文本连接。

【讨论】：