计算基因序列中ATCG的含量以及碱基motif的绘制

1、ATCG含量计算

• 来源我在学习Modern Statistics for Modern Biology 此文中的《Modern Statistics for Modern Biology》Chapter 二: 统计建模（2.4-2.5）

读取fasta序列文件

setwd("e://compute language/NGS/Modern Statistics for Modern Biology/data/")  
> library(Biostrings)
> staph = readDNAStringSet("staphsequence.ffn.txt", "fasta") ## 读取fasta文件

fastat文件格式如下

>a
ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCTGTAAGTTACT
CAACTTTCCTAAAAGATACTGAGCTTTACACGATCAAAGATGGTGAAGCTATCGTATTATCGAGTATTCC
TTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTTGTAGGC
TATGAAGTAAAACCTCACTTTATTACTACTGAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTC
CAAAAGAAGCAACAAAACCTTCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAA

单个基因计算

> staph[1]
  A DNAStringSet instance of length 1
    width seq                                                                        names               
[1]  1362 ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAA...TAGAGAATCTTGAAAAAGAAATAAGAAATGTATAA lcl|NC_002952.2_c...
> letterFrequency(staph[[1]], letters = "ACTG", OR = 0)
  A   C   T   G 
522 219 392 229

多个基因计算

• 这里活用了apply函数，更多参考搜索或者参考这个 掌握R语言中的apply函数族

> letterFrq = vapply(staph, letterFrequency, FUN.VALUE = numeric(4), letters = "ACGT", OR = 0)
> colnames(letterFrq) = paste0("gene", seq(along = staph))
> computerProportions = function(x){x/sum(x)}
> prop10 = apply(tab10, 2, computerProportions) ## 2表示列
> round(prop10, digits = 2)
  gene1 gene2 gene3 gene4 gene5 gene6 gene7 gene8 gene9 gene10
A  0.38  0.36  0.35  0.37  0.35  0.33  0.33  0.34  0.38   0.27
C  0.16  0.16  0.13  0.15  0.15  0.15  0.16  0.16  0.14   0.16
G  0.17  0.17  0.23  0.19  0.22  0.22  0.20  0.21  0.20   0.20
T  0.29  0.31  0.30  0.29  0.27  0.30  0.30  0.29  0.28   0.36
> p0 = rowMeans(prop10)
> p0
        A         C         G         T 
0.3470531 0.1518313 0.2011442 0.2999714 

2、motif绘制

• 来源我在学习Modern Statistics for Modern Biology 此文中的《Modern Statistics for Modern Biology》Chapter 二 统计建模（2.6 - 2.8）

> setwd("e://compute language/NGS/Modern Statistics for Modern Biology/data/")
> library("seqLogo")
载入需要的程辑包：grid
Warning message:
程辑包‘seqLogo’是用R版本3.5.1 来建造的 
> load("kozak.RData")
> kozak
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A 0.33 0.25  0.4 0.15 0.20    1    0    0 0.05
C 0.12 0.25  0.1 0.40 0.40    0    0    0 0.05
G 0.33 0.25  0.4 0.20 0.25    0    0    1 0.90
T 0.22 0.25  0.1 0.25 0.15    0    1    0 0.00
> pwm = makePWM(kozak)
> seqLogo(pwm, ic.scale = FALSE)