Using forloop to add headers to multiple files

Hi guys! I need help in setting a for loop in R (I'm quite new programming in R). I would like to add the same header to all the files that match a concrete pattern inside a folder.

To get the list of files I'm using the following code:

filelist <- list.files(pattern = "DESeq2_result*")

And this is the for loop I am trying to implement:

for (i in seq_along(filelist)) {
   names[[i]] <- a
   out [i]

}

where a is a vector that I defined with the names of the different columns:

a <- c("gene_id", "baseMean", "log2FC",
       "SD", "WaldStatistic", "pval", "padj")

If you have any tutorial/page to help me to learn and practise my ability to code functions and loops in R would be so much appreciated.

Thank you so much in advance!

Jordi

• 4,981 views • link

updated 7.5 years ago by Arup Ghosh

• written 7.5 years ago by jordi.planells

What error do you get? What is it that you would like to get out of the loop? The same files but now with change of header?

• 1 views • link

written 7.5 years ago by Benn

3 answers

As I understood, you want to open some files containing the pattern "DESeq2_result*" as data.frames in a list, assigning new names to the columns of these dataframes based on the a vector, and maybe name the elements of the list based on the files name? You can do it that way:

filelist <- list.files(pattern = "DESeq2_result")

a <- c("gene_id", "baseMean", "log2FC",
       "SD", "WaldStatistic", "pval", "padj")

data<-list()

for (i in 1:length(filelist)) {
  data[[i]]<-read.table(filelist[i])
  colnames(data[[i]])<-a
}

names(data)<-filelist

for (i in 1:length(data)) {
    output_name <- paste0("colnames_",names(data[i]))
    write.table(data[[i]], output_name, quote = F, row.names = F, col.names = T, sep="\t")
}

EDIT: added the write.table part to take your comment into account in order to export the imported files with the column names.

• 1 views • link

written 7.5 years ago by Gautier Richard

Basically, what i want to do is to add column names to my files, in one piece of code. For a single file, the code would be:

data <- read.table("file", sep = "\t", header = FALSE)
names(data)
colnames(data) <- a
write.table(data, "file", sep = "\t", col.names = TRUE, row.names = FALSE)

I'm trying to optimise my code, so I can do all of them without having to type in my Rmarkdown document 8 times the same code (one for each file)

• 1 views • link

written 7.5 years ago by jordi.planells

Ok, I modified the code so it does what you want.

I think that a much better way would be to simply replace the first line of every file with a shell script or a one-liner. You don't need R for that. The code above is really heavy for what you need. Pasting the first line stored in file a at the beginning of every file with pattern would be much more efficient, but not R-based.

• 1 views • link

written 7.5 years ago by Gautier Richard

Ok thank you so much! So basically you are suggesting me to do this with a shell for loop and sed/awk command instead. Thank you so much again for your help! Cheers!

• 1 views • link

written 7.5 years ago by jordi.planells

Use col.names = argument when reading the files, then write out, something like this:

for(i in list.files(pattern = "DESeq2_result_*"))
  write.table(read.table(i, col.names = c("gene_id", "baseMean", "log2FC",
                                          "SD", "WaldStatistic", "pval", "padj")), i)

Note: this overwrites existing files, to create new files:

for(i in list.files(pattern = "DESeq2_result_*"))
  write.table(read.table(i, col.names = c("gene_id", "baseMean", "log2FC",
                                          "SD", "WaldStatistic", "pval", "padj")),
              paste0(i, ".fixed.txt"))

• 1 views • link

written 7.5 years ago by zx8754

Thank you a lot!! It is really appreciated

• 1 views • link

written 7.5 years ago by jordi.planells

Creates a new file with headers. Change the gsub pattern before using.

col=c("gene_id", "baseMean", "log2FC","SD", "WaldStatistic", "pval", "padj")
for(file in list.files(pattern="^DESeq2_result*")){
  write.table(read.table(file,col.names = col),
              paste0("updated_",gsub(pattern = "\\.txt$", "", file),".tsv"),col.names = TRUE, row.names = FALSE,sep="\t") #Also update the file extension
}

• 1 views • link

written 7.5 years ago by Arup Ghosh

Thank you too, arup!

• 1 views • link

written 7.5 years ago by jordi.planells