如何從不同的文件中提取相同的數據

Question

為了從 qiime2 工件中提取頻率表並將其寫入 tsv output，您必須：

rel_freq_table <- read_qza("05.TaxonomyClassification/rel_freq/1_rel_freq_table.qza")
rel_freq_table <- data.frame(rel_freq_table$data)
rel_freq_table <-  setDT(rel_freq_table, keep.rownames = TRUE )
colnames(rel_freq_table)[1]<- c( "Feature.ID" )
write.table(rel_freq_table, file = "1_rel_freq_table.tsv", row.names = FALSE, dec = ",")

現在，我有七個 qiime2 工件

rel_freqs <- c("05.TaxonomyClassification/rel_freq/1_rel_freq_table.qza","05.TaxonomyClassification/rel_freq/2_rel_freq_table.qza",
           "05.TaxonomyClassification/rel_freq/3_rel_freq_table.qza","05.TaxonomyClassification/rel_freq/4_rel_freq_table.qza",
           "05.TaxonomyClassification/rel_freq/5_rel_freq_table.qza","05.TaxonomyClassification/rel_freq/6_rel_freq_table.qza",
           "05.TaxonomyClassification/rel_freq/7_rel_freq_table.qza")

我想自動化這個過程，所以我只需要運行一次命令。 我試過循環和 lapply 但沒有運氣，有人知道嗎？

Answer 1

您可以編寫 function 並使用lapply將其應用於每個文件：

read_qiime2_write_tsv <- function(filename) {
  rel_freq_table <- read_qza(filename)
  rel_freq_table <- data.frame(rel_freq_table$data)
  rel_freq_table <-  setDT(rel_freq_table, keep.rownames = TRUE )
  colnames(rel_freq_table)[1]<- c( "Feature.ID" )
  write.table(rel_freq_table, 
          file = paste0(tools::file_path_sans_ext(basename(filename)), '.tsv'), 
          row.names = FALSE, dec = ",")
}

lapply(rel_freqs, read_qiime2_write_tsv)