初识R语言之条件循环篇

原创

王小王_123 2022-06-29 17:19:30 博主文章分类：R语言从入门到科研 ©著作权

文章标签 r语言开发语言 R语言循环 R语言条件判断 sed 文章分类 运维

©著作权归作者所有：来自51CTO博客作者王小王_123的原创作品，请联系作者获取转载授权，否则将追究法律责任

pool = 1:10
for(fish in pool){
  print(fish)
}

初识R语言之条件循环篇_开发语言

通过循环操作读取文件并进行数据的处理

files = c('DEG1.xls', 'DEG2.xls', 'DEG3.xls', 'DEG4.xls')
n = 1
for(file in files){
  print(paste0('DEG unfiltered file is ', file))
  # 1 reading DEG unfiltered file
  df = read.delim(file, header = T, sep = '\t')
  
  # 2 filtering different expressed genes
  df$logFC = log2(df$FC)
  deg = subset(df, abs(logFC) > 1 & pval < 0.05)
  
  # 3 reading TF annotation file
  TF = read.delim('Homo_sapiens_TF.txt', header = T, sep = '\t')
  
  # 4 annotate DEGs with TF family information
  deg_TF_all = merge(deg, TF, 
                     by.x = 'id', 
                     by.y = 'Symbol',
                     all.x = T)  
  
  # 5 output annotated DEGs
  outfile_name = paste0('deg_TF_', n, '.xls')
  write.table(deg_TF_all, outfile_name,
              col.names = T, row.names = F,
              sep = '\t', quote = F)
  n = n + 1
}

判断

a = 2
b = 3
c = 1
if(a > b){
  print('a > b')
}


if(a > b){
  print('a > b')
} else {
  print('a <= b')
}

if(a > b){
  print('a > b')
} else if(a > c){
  print('a > c')
} else {
  print('a <= b and a <= c')
}

基本语法和java与C语言有点类似，思想和Python相符合

批量处理4个文件：差异筛选+TF注释

如果已经加载TF数据库，则不再读取

files = c('DEG1.xls', 'DEG2.xls', 'DEG3.xls', 'DEG4.xls')
n = 1
for(file in files){
  print(paste0('Processing file is ', file))
  # 1 reading DEG unfiltered file 
  df = read.delim(file, header = T, sep = '\t')
  
  # 2 filtering different expressed genes
  df$logFC = log2(df$FC)
  deg = subset(df, abs(logFC) > 1 & pval < 0.05)
  
  if(exists('TF')){
    print('TF database has already existed')
  } else {
    # 3 reading TF annotation file 
    TF = read.delim('Homo_sapiens_TF.txt', header = T, sep = '\t')
  }
  
  # 4 annotate DEGs with TF family information
  deg_TF_all = merge(deg, TF, 
                     by.x = 'id', 
                     by.y = 'Symbol',
                     all.x = T)  
  
  # 5 output annotated DEGs 
  outfile_name = paste0('deg_TF_', n, '.xls')
  write.table(deg_TF_all, outfile_name,
              col.names = T, row.names = F,
              sep = '\t', quote = F)
  n = n + 1
}