在 R 的一个文件夹中的多个 .txt 文件上运行循环

Question

我有一个脚本可以计算拷贝数变异并将数据保存到基于第一列信息的名为“genesforcomp1”的现有文件中。输入文件名为 BRCA1.txt、BRCA2.txt、BRCA3.txt.......BRCA4376.txt。另一个输入文件“genes.txt”在每个循环中都是相同的，用于注释，而“genesforcomp1”用于更新输出。 由于文件很多，我想知道是否可以通过R中的循环函数来完成。 这是我的脚本

setwd("/home/sumit/Test/1_Lung/AllCNV/0a0bd4cc-3da8-44ff-ba08-a7e86b95f2f6/aa")
library(GenomicRanges)
library(dplyr)
library("scales")
require(tidyverse)
#Create annotation or refrence table
genes <- read.table("/home/sumit/Test/1_Lung/AllCNV/0a0bd4cc-3da8-44ff-ba08-a7e86b95f2f6/genes.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)
genes$chromosome_name <- gsub('X', '23', genes$chromosome_name)
genes$chromosome_name <- gsub('Y', '24', genes$chromosome_name)
colnames(genes) <- c("GeneSymbol","Chr","Start","End")
genes_GR <- makeGRangesFromDataFrame(genes,keep.extra.columns = TRUE)
#File need to be analyzed (3 step: preprocessing, comparison with reference or annotation and post-porcessing)
df<- read.table("BRCA1.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)
df$Chromosome <- gsub('X', '23', df$Chromosome)
df$Chromosome <- gsub('Y', '24', df$Chromosome)
colnames(df) <- c("Barcode", "Chr", "Start", "End", "extra1", "extra2")
cnv <-  makeGRangesFromDataFrame(df, keep.extra.columns = TRUE)
hits <- findOverlaps(genes_GR, cnv, type="within")
df_ann <- cbind(df[subjectHits(hits),],genes[queryHits(hits),])
df_ann <- unique(df_ann)
df_ann <- df_ann[ , c("GeneSymbol", "Chr", "extra2")]
colnames(df_ann) <- c("Ensembl_ID","Chr","Seg_value")
df_ann$Seg_value2 <- abs(df_ann$Seg_value)
df_ann$Seg_value2 = 2^df_ann$Seg_value2
df_ann$Seg_value2 = df_ann[, 4] - 1
df_ann$Seg_value2 = df_ann[, 4] * 2
df_ann$Seg_value2 <- with(df_ann, sign(Seg_value) * Seg_value2)
df_ann <- df_ann[ , c("Ensembl_ID", "Seg_value")]
df_ann$Seg_value <- rescale(df_ann$Seg_value, to = c(-1, 1))
df_ann1 <- read.table("/home/sumit/Academic/DHR/TCGA/Gene List/Final1/genesbase.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)
df <- rbind.data.frame(df_ann, df_ann1)
df <- df[!duplicated(df$Ensembl_ID),]
#saving the results into existing file based on first column values
df1 <- read.delim("genesforcomp1", check.names=FALSE, stringsAsFactors=FALSE)
lst <- list(data.frame(df1), data.frame(df))
df2 <- reduce(lst, full_join, by = "Ensembl_ID") %>% replace(., is.na(.), 0);
write.table(df2, file="genesforcomp1", quote = F, sep = "\t", row.names = F)

任何关于如何循环脚本的建议或想法将不胜感激。提前致谢！

Answer 1

由于您的文件名遵循良好的模式，您可以执行从 1 到 4376 的循环，并将代码中的 "BRCA1.txt" 替换为 paste0("BRCA", i, ".txt")。可能有一些方法可以在不对模式进行硬编码的情况下进行循环，但在您的情况下，您似乎不需要它。

setwd("/home/sumit/Test/1_Lung/AllCNV/0a0bd4cc-3da8-44ff-ba08-a7e86b95f2f6/aa")
library(GenomicRanges)
library(dplyr)
library("scales")
require(tidyverse)
#Create annotation or refrence table
genes <- read.table("/home/sumit/Test/1_Lung/AllCNV/0a0bd4cc-3da8-44ff-ba08-a7e86b95f2f6/genes.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)
genes$chromosome_name <- gsub('X', '23', genes$chromosome_name)
genes$chromosome_name <- gsub('Y', '24', genes$chromosome_name)
colnames(genes) <- c("GeneSymbol","Chr","Start","End")
genes_GR <- makeGRangesFromDataFrame(genes,keep.extra.columns = TRUE)
#File need to be analyzed (3 step: preprocessing, comparison with reference or annotation and post-porcessing)
for(i in 1:4376){
  df<- read.table(paste0("BRCA", i, ".txt"), sep="\t", stringsAsFactors=FALSE, header=TRUE)
  df$Chromosome <- gsub('X', '23', df$Chromosome)
  df$Chromosome <- gsub('Y', '24', df$Chromosome)
  colnames(df) <- c("Barcode", "Chr", "Start", "End", "extra1", "extra2")
  cnv <-  makeGRangesFromDataFrame(df, keep.extra.columns = TRUE)
  hits <- findOverlaps(genes_GR, cnv, type="within")
  df_ann <- cbind(df[subjectHits(hits),],genes[queryHits(hits),])
  df_ann <- unique(df_ann)
  df_ann <- df_ann[ , c("GeneSymbol", "Chr", "extra2")]
  colnames(df_ann) <- c("Ensembl_ID","Chr","Seg_value")
  df_ann$Seg_value2 <- abs(df_ann$Seg_value)
  df_ann$Seg_value2 = 2^df_ann$Seg_value2
  df_ann$Seg_value2 = df_ann[, 4] - 1
  df_ann$Seg_value2 = df_ann[, 4] * 2
  df_ann$Seg_value2 <- with(df_ann, sign(Seg_value) * Seg_value2)
  df_ann <- df_ann[ , c("Ensembl_ID", "Seg_value")]
  df_ann$Seg_value <- rescale(df_ann$Seg_value, to = c(-1, 1))
  df_ann1 <- read.table("/home/sumit/Academic/DHR/TCGA/Gene List/Final1/genesbase.txt", sep="\t", stringsAsFactors=FALSE, header=TRUE)
  df <- rbind.data.frame(df_ann, df_ann1)
  df <- df[!duplicated(df$Ensembl_ID),]
  #saving the results into existing file based on first column values
  df1 <- read.delim("genesforcomp1", check.names=FALSE, stringsAsFactors=FALSE)
  lst <- list(data.frame(df1), data.frame(df))
  df2 <- reduce(lst, full_join, by = "Ensembl_ID") %>% replace(., is.na(.), 0);
  write.table(df2, file="genesforcomp1", quote = F, sep = "\t", row.names = F)
}