This is a test version of Biostars. For the public version, visit https://www.biostars.org.
file handling in R

i want to extract gene column (2nd column of every file) from multiple text files and merge them to get unique gene list. But in every text file number of rows differs. can someone please tell me how to write R code for this? Thanks in advance

r
• 1,515 views • link
updated by bioinformatics2020 bioinformatics2020 • written by smrutimayipanda • smrutimayipanda

2 answers

Your could use lapply with rbind, or just use cut/awk followed by sort -u on the shell. There's no need for R here.

• 0 views • link
written by Ram Ram 
if(!require("tidyverse")) install.packages("tidyverse")
files <- purrr::map_dfr(list.files(pattern = "\\.txt$"), read_tsv)

Then if you only want the Genes column:

files <- files$Genes
• 0 views • link
written by bioinformatics2020 bioinformatics2020

It will work either way, but with the map functions in this case you can just put the name of the function at the end. You don't need to call it as an anonymous function. Also, you should escape the period in the file extension, otherwise it would match any character. I usually put an end of line in the regex too for good measure.

files <- purrr::map_dfr(list.files(pattern = "\\.txt$"), read_tsv)
• 0 views • link
written by rpolicastro rpolicastro

No problem, just spreading the R love!

• 0 views • link
written by rpolicastro rpolicastro

Log in to answer this question.

More posts like this