R语言Biostrings包函数介绍（一）

一、定义的常量

> DNA_BASES 
[1] "A" "C" "G" "T"
> RNA_BASES 
[1] "A" "C" "G" "U"
> GENETIC_CODE 
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" 
CTC CTA CTG CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC 
"L" "L" "L" "P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" 
ATA ATG ACT ACC ACA ACG AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA 
"I" "M" "T" "T" "T" "T" "N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" 
GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA GGG 
"V" "A" "A" "A" "A" "D" "D" "E" "E" "G" "G" "G" "G" 
attr(,"alt_init_codons")
[1] "TTG" "CTG"
> RNA_GENETIC_CODE
UUU UUC UUA UUG UCU UCC UCA UCG UAU UAC UAA UAG UGU UGC UGA UGG CUU 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" 
CUC CUA CUG CCU CCC CCA CCG CAU CAC CAA CAG CGU CGC CGA CGG AUU AUC 
"L" "L" "L" "P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" 
AUA AUG ACU ACC ACA ACG AAU AAC AAA AAG AGU AGC AGA AGG GUU GUC GUA 
"I" "M" "T" "T" "T" "T" "N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" 
GUG GCU GCC GCA GCG GAU GAC GAA GAG GGU GGC GGA GGG 
"V" "A" "A" "A" "A" "D" "D" "E" "E" "G" "G" "G" "G" 
attr(,"alt_init_codons")
[1] "UUG" "CUG"
> AMINO_ACID_CODE
    A     R     N     D     C     Q     E     G     H     I     L 
"Ala" "Arg" "Asn" "Asp" "Cys" "Gln" "Glu" "Gly" "His" "Ile" "Leu" 
    K     M     F     P     S     T     W     Y     V     U     O 
"Lys" "Met" "Phe" "Pro" "Ser" "Thr" "Trp" "Tyr" "Val" "Sec" "Pyl" 
    B     J     Z     X 
"Asx" "Xle" "Glx" "Xaa" 
> IUPAC_CODE_MAP
     A      C      G      T      M      R      W      S      Y      K 
   "A"    "C"    "G"    "T"   "AC"   "AG"   "AT"   "CG"   "CT"   "GT" 
     V      H      D      B      N 
 "ACG"  "ACT"  "AGT"  "CGT" "ACGT" 

用于核酸和蛋白序列比对的取代矩阵，这些数据需用户自行载入（最后三个是函数，但可以不设参数）：data(BLOSUM45/50/62/80/100)、data(PAM30/40/70/120/250)、nucleotideSubstitutionMatrix()、qualitySubstitutionMatrices()、errorSubstitutionMatrices()

二、包含单一序列的类

1. XString是一种虚拟类，派生出BString、DNAString、RNAString和AAString类。
2. BString类是一个用于存储大字符串(长字符序列)并使其操作简单而有效的通用容器。DNAString、RNAString和AAString类是类似的容器，但更侧重于存储DNA序列(DNAString)、RNA序列(RNAString)或氨基酸序列(AAString)。
3. XString对象和标准字符串向量之间的两个主要区别是:(1)存储在XString对象中的数据不会在对象复制时复制和(2)一个XString对象只能存储一个字符串(参见XStringSet容器的一种有效的方式将一个大的字符串集合存储在一个单独的对象)。

示例：（以下对象x均为XString）

1. BString(x="", start=1, nchar=NA)：试图将x转换成BString类对象，方法是读取从x的起始位置开始的nchar字母。
2. alphabet(x)：查看XString对象可接受哪些字母，若超出范围会报错。

> alphabet(BString())
NULL
> alphabet(DNAString())
 [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K"
[11] "V" "H" "D" "B" "N" "-" "+" "."
> alphabet(RNAString())
 [1] "A" "C" "G" "U" "M" "R" "W" "S" "Y" "K"
[11] "V" "H" "D" "B" "N" "-" "+" "."
> alphabet(AAString())
 [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I"
[11] "L" "K" "M" "F" "P" "S" "T" "W" "Y" "V"
[21] "U" "O" "B" "J" "Z" "X" "*" "-" "+" "."

3. length(x) or nchar(x)：XString对象的长度，即字母个数
4. as.character(x) or toString(x)：将x由XString类转换为普通字符串。
5. x[ i ]：索引同样适用。

> b <- BString("I am a BString object")
> b
  21-letter "BString" instance
seq: I am a BString object
> as.character(b)
[1] "I am a BString object" #注意普通字符串与XString的区别
> length(b) #在普通字符串向量中，length指向量个数
[1] 21
> nchar(b) #尽量使用length()，效率更高
[1] 21
> b[1]
  1-letter "BString" instance
seq: I
> b[7:12]
  6-letter "BString" instance
seq:  BStri
> b[]
  21-letter "BString" instance
seq: I am a BString object
> b[length(b):1]
  21-letter "BString" instance
seq: tcejbo gnirtSB a ma I

6. x1 == x2：判断两个XString之间是否相同，返回一个逻辑值；要求同类，但DNAString可与RNAString比较。 当==的两边不属于同一个类时，则属于最低类的边首先转换为属于另一个类(最高类)的一个对象。类(伪)顺序是character< BString < DNAString。

> DNAString()==RNAString()
[1] TRUE
> DNAString('ACGT')==RNAString('ACGU') #该种比较T=U
[1] TRUE
> DNAString('ACGT')==RNAString('GCUU')
[1] FALSE
> DNAString('ACGT')==RNAString('ACGG')
[1] FALSE
> BString('ABCD')=='ABCD'
[1] TRUE
> BString('ACGT')==DNAString('ACGT')
Error in BString("ACGT") == DNAString("ACGT") : 
  comparison between a "BString" instance and a "DNAString" instance is not supported

三、XStringViews类及其索引

XStringViews类由通过继承Views类（IRanges包定义）而来，XStringViews类对象用于存储同一条序列（目标序列）上的一系列“视野”，即序列区域或子序列。每一个视野由起始点（start）和终止点（end）确定，也隐含了序列的长度信息。

示例：

> d <- DNAString("TTGAAAA-CTC-N")
> dd2 <- subseq(d, start=8)
> v4 <- Views(dd2, start=3:0, end=5:8)
> v4
  Views on a 6-letter DNAString subject
subject: -CTC-N
views:
    start end width
[1]     3   5     3 [TC-]
[2]     2   6     5 [CTC-N]
[3]     1   7     7 [-CTC-N ]
[4]     0   8     9 [ -CTC-N  ] #最后2行超出限制
> length(v4)
[1] 4
> v4[4:2]
  Views on a 6-letter DNAString subject
subject: -CTC-N
views:
    start end width
[1]     0   8     9 [ -CTC-N  ]
[2]     1   7     7 [-CTC-N ]
[3]     2   6     5 [CTC-N]
> v4[2] #索引单个元素仍为XStringViews类
  Views on a 6-letter DNAString subject
subject: -CTC-N
views:
    start end width
[1]     2   6     5 [CTC-N]
> v4[[2]] #两个方括号，返回XString类
  5-letter "DNAString" instance
seq: CTC-N
> v4[[3]] #超出限制，故报错
Error in getListElement(x, i, ...) : view is out of limits
> v4[-3]
  Views on a 6-letter DNAString subject
subject: -CTC-N
views:
    start end width
[1]     3   5     3 [TC-]
[2]     2   6     5 [CTC-N]
[3]     0   8     9 [ -CTC-N  ]
> v4[c(TRUE,FALSE,TRUE,FALSE)]
  Views on a 6-letter DNAString subject
subject: -CTC-N
views:
    start end width
[1]     3   5     3 [TC-]
[2]     1   7     7 [-CTC-N ]

四、包含多个序列集的类

1. BStringSet类是一个容器，用于存储一组BString对象，并使其操作简单而高效。
2. 类似地，DNAStringSet(或RNAStringSet，或AAStringSet)类是用于存储一组DNAString(或RNAString，或AAStringSet)对象的容器。
3. 所有这些容器都直接从XStringSet虚拟类派生。

BStringSet(x=character(), start=NA, end=NA, width=NA, use.names=TRUE)

示例：

> x0 <- c("#CTC-NACCAGTAT", "#TTGA", "TACCTAGAG")
> x0
[1] "#CTC-NACCAGTAT" "#TTGA"         
[3] "TACCTAGAG"     
> width(x0)
[1] 14  5  9
> x1 <- BStringSet(x0)
> x1
  A BStringSet instance of length 3
    width seq
[1]    14 #CTC-NACCAGTAT
[2]     5 #TTGA
[3]     9 TACCTAGAG
> BStringSet(x0, start=4, end=-3)
  A BStringSet instance of length 3
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> subseq(x1, start=4, end=-3)
  A BStringSet instance of length 3
    width seq
[1]     9 C-NACCAGT
[2]     0 
[3]     4 CTAG
> dna0 <- DNAStringSet(x0, start=4, end=-3)
> names(dna0)
NULL
> names(dna0)[2] <- "seqB"
> dna0
  A DNAStringSet instance of length 3
    width seq                 names               
[1]     9 C-NACCAGT           <NA>
[2]     0                     seqB
[3]     4 CTAG                <NA>

五、基本转换

1. DNA中T→U变为RNA：

> dna <- DNAString('ATTGCATACCATAGG')
> dna
  15-letter "DNAString" instance
seq: ATTGCATACCATAGG
> RNAString(dna)
  15-letter "RNAString" instance
seq: AUUGCAUACCAUAGG

2. 互补

> complement(dna)
  15-letter "DNAString" instance
seq: TAACGTATGGTATCC

3. 反向及反向互补

> dna
  15-letter "DNAString" instance
seq: ATTGCATACCATAGG
> rev(dna) #反向
  15-letter "DNAString" instance
seq: GGATACCATACGTTA
> reverseComplement(dna) #反向互补
  15-letter "DNAString" instance
seq: CCTATGGTATGCAAT

4. 转录

> dna
  15-letter "DNAString" instance
seq: ATTGCATACCATAGG
> rna <- RNAString(complement(dna))
> rna
  15-letter "RNAString" instance
seq: UAACGUAUGGUAUCC

5. RNA中U→T转为DNA

> dna
  15-letter "DNAString" instance
seq: ATTGCATACCATAGG
> DNAString(rna)
  15-letter "DNAString" instance
seq: TAACGTATGGTATCC

6. RNA逆转录为cDNA

> rna
  15-letter "RNAString" instance
seq: UAACGUAUGGUAUCC
> cDNA <- DNAString(complement(rna))
> cDNA
  15-letter "DNAString" instance
seq: ATTGCATACCATAGG

注意：转录和逆转录需要套用两层：RNAString(complement(dna))和DNAString(complement(rna))。

7. 密码子

> codons(rna)
  Views on a 15-letter RNAString subject
subject: UAACGUAUGGUAUCC
views:
    start end width
[1]     1   3     3 [UAA]
[2]     4   6     3 [CGU]
[3]     7   9     3 [AUG]
[4]    10  12     3 [GUA]
[5]    13  15     3 [UCC]

8. 翻译

> translate(rna)
  5-letter "AAString" instance
seq: *RMVS

9. 统计字母频率

> alphabetFrequency(dna)
A C G T M R W S Y K V H D B N - + . 
5 3 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
> letterFrequency(dna,letters = 'CG')
C|G 
  6 
> GC <- letterFrequency(dna,'CG')/letterFrequency(dna,'AGCT')
> GC
C|G 
0.4 

10. 搜索匹配格式

> matchPattern('CA',dna)
  Views on a 15-letter DNAString subject
subject: ATTGCATACCATAGG
views:
    start end width
[1]     5   6     2 [CA]
[2]    10  11     2 [CA]

部分参考：https://blog.csdn.net/u014801157/article/details/24372449（侵删）