R语言初级题作业笔记

题目链接：http://www.bio-info-trainee.com/3793.html
题目比较基础，我这里就不附加详细的注释了
> rm(list = ls())
> options(stringsAsFactors = F)
> a=read.table('SraRunTable.txt',sep = '\t',header = T)
> b=read.csv('sample.csv')
> colnames(a)
 [1] "BioSample"          "Experiment"         "MBases"             "MBytes"             "Run"               
 [6] "SRA_Sample"         "Sample_Name"        "Assay_Type"         "AssemblyName"       "AvgSpotLen"        
[11] "BioProject"         "Center_Name"        "Consent"            "DATASTORE_filetype" "DATASTORE_provider"
[16] "InsertSize"         "Instrument"         "LibraryLayout"      "LibrarySelection"   "LibrarySource"     
[21] "LoadDate"           "Organism"           "Platform"           "ReleaseDate"        "SRA_Study"         
[26] "age"                "cell_type"          "marker_genes"       "source_name"        "strain"            
[31] "tissue"            
> colnames(b)
 [1] "Accession"           "Title"               "Sample.Type"         "Taxonomy"            "Channels"           
 [6] "Platform"            "Series"              "Supplementary.Types" "Supplementary.Links" "SRA.Accession"      
[11] "Contact"             "Release.Date"       
> d=merge(a,b,by.x = 'Sample_Name',by.y = 'Accession')
> e=d[,c("MBases","Title")]
> save(e,file = 'input.Rdata')
> rm(list = ls())
> options(stringsAsFactors = F)
> load(file = 'input.Rdata')
> e[,2]
  [1] "SS2_15_0048_A1"  "SS2_15_0048_A2"  "SS2_15_0048_A3"  "SS2_15_0048_A4"  "SS2_15_0048_A5"  "SS2_15_0048_A6" 
  [7] "SS2_15_0048_A7"  "SS2_15_0048_A8"  "SS2_15_0048_A9"  "SS2_15_0048_A10" "SS2_15_0048_A11" "SS2_15_0048_A12"
 [13] "SS2_15_0048_A13" "SS2_15_0048_A14" "SS2_15_0048_A15" "SS2_15_0048_A16" "SS2_15_0048_A17" "SS2_15_0048_A18"
···
> plate=unlist(lapply(e[,2],function(x){
+   # x=e[1,2]
+   x
+   strsplit(x,'_')[[1]][3]
+   
+ }))
> table(plate)
plate
0048 0049 
 384  384 
> boxplot(e[,1]~plate)
> t.test(e[,1]~plate)

    Welch Two Sample t-test

data:  e[, 1] by plate
t = 2.3019, df = 728.18, p-value = 0.02162
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 0.1574805 1.9831445
sample estimates:
mean in group 0048 mean in group 0049 
          13.08854           12.01823 

> e$plate=plate
> library(ggplot2)
> colnames(e)
[1] "MBases" "Title"  "plate" 
> ggplot(e,aes(x=plate,y=MBases))+geom_boxplot()
> library(ggpubr)
载入需要的程辑包：magrittr
> p <- ggboxplot(e, x = "plate", y = "MBases",
+                color = "plate", palette = "jco",
+                add = "jitter")
> 
> 
> # Add p-value
> p + stat_compare_means(method = 't.test')
1.png
2.png
3.png