学习总结

时间：2017.9.3
内容：初级10 个题目：http://www.bio-info-trainee.com/3793.html

新建6个向量

> c1 <- 1:10
> c2 <- c('a','b','c','d','e','f')
> c3 <- c(T,F,T,F,T)
> c4 <- seq(10,20,1)
> c5 <- rep(x = c(1,2,3),times=3)
> c6 <- paste(c1,c2,c3,sep = '')
> c1
 [1]  1  2  3  4  5  6  7  8  9 10
> c2
[1] "a" "b" "c" "d" "e" "f"
> c3
[1]  TRUE FALSE  TRUE FALSE  TRUE
> c4
 [1] 10 11 12 13 14 15 16 17 18 19 20
> c5
[1] 1 2 3 1 2 3 1 2 3
> c6
 [1] "1aTRUE"  "2bFALSE" "3cTRUE"  "4dFALSE" "5eTRUE"  "6fTRUE"  "7aFALSE" "8bTRUE" 
 [9] "9cFALSE" "10dTRUE"

运行getwd()

 getwd()
[1] "C:/Users/86157/Desktop/珠海生信学习/长春_R/3天培训_R"

新建数据结构

> a1 <- matrix(1:20,nrow=5,ncol=4)
> a1
     [,1] [,2] [,3] [,4]
[1,]    1    6   11   16
[2,]    2    7   12   17
[3,]    3    8   13   18
[4,]    4    9   14   19
[5,]    5   10   15   20

> date<-c(21,22,23,35,52)
> plan<-c('mon','tue','wed','thur','fri')
> color<-c('green','red','white','black','purple')
> a2<-data.frame(date,plan,color)
> a2
  date plan  color
1   21  mon  green
2   22  tue    red
3   23  wed  white
4   35 thur  black
5   52  fri purple

> g<-'Hello world'
> h<-1:5
> j<-matrix(1:10,nrow=5,ncol=2)
> f<-c('mon','tue','wed')
> r_list<-list(flag=g,h,j,f)
> r_list
$flag
[1] "Hello world"

[[2]]
[1] 1 2 3 4 5

[[3]]
     [,1] [,2]
[1,]    1    6
[2,]    2    7
[3,]    3    8
[4,]    4    9
[5,]    5   10

[[4]]
[1] "mon" "tue" "wed"

查看内置数据集

data()

image.png

rivers

image.png

将RunInfo Table文件读入R

SraRunTable <- read.csv(file = 'SraRunTable.csv',header = T,sep = ',')

image.png

sample <- read.csv(file = 'sample.csv',header = T,sep = ',')

image.png

将SraRunTable与sample关联起来

merge <- merge(SraRunTable,sample,by.x = 'Sample_Name',by.y = 'Accession')

把前面读取的样本信息表格的样本名字根据下划线分割看第3列元素的统计情况

> e<- merge[,c("MBases","Title")]
> b <- as.character(e[,2])##strsplit函数只能对字符串进行操作
> plate=unlist(lapply(b,function(x){
+   # x=e[1,2]
+   x
+   strsplit(x,'_')[[1]][3]
+   
+ }))

image.png

分组绘制箱线图(boxplot)，频数图(hist)，以及密度图(density)

箱图

> boxplot(e[,1]~plate)

image.png