批量将多个文件内的压缩文件复制至一个文件内

有感于 果子学生信

应用：从TCGA GDC中下载下来的文件进行汇总

library(TCGAbiolinks)

query <- GDCquery(project = "TCGA-LUSC",

                    data.category = "Transcriptome Profiling",

                    data.type = "Gene Expression Quantification",

                    workflow.type = "HTSeq - Counts" )

  GDCdownload(query)

  

# 所有下载的counts数据存在“./GDCdata/TCGA-LUSC/harmonized/Transcriptome_Profiling”;

# 并且被保存在一个个文件夹内

# 接下来首先将每个文件夹内的文件转自一个文件内"./expr_data/raw_data_in_one"

dirname <- "001a2541-a9d3-4811-97bf-d8fcd89b4c66"

for (dirname in dir("./GDCdata/TCGA-LUSC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/")) {

  ## use list.files function to find single file within “./GDCdata/TCGA-LUSC/harmonized/Transcriptome_Profiling”

  file <- list.files(path = paste0(getwd(),

                                   "/GDCdata/TCGA-LUSC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/",

                                   dirname),pattern = "*.counts.gz") #找到文件中的内容，pattern可以是正则表达式

  ## 使用file.copy函数复制黏贴压缩文件到raw_data_in_one

  file.copy(paste0(getwd(),"/GDCdata/TCGA-LUSC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/",

                   dirname,"/",file),to = "./expr_data/raw_data_in_one") #复制内容到新的文件夹

}