Merging HTseq files

Question

[makwana.kd]

Hi, I have been trying to merge HTseq files into one data matrix using following script. However, I am encountering following error;

directory <- "C/RNA SEQ adv cgrp/IWAT"

sampleFiles <- grep("COUNT FILES",list.files(directory),value=TRUE)

 condition <- c('237 COUNT FILES','264 COUNT FILES','267 COUNT FILES','265 COUNT FILES')


sampleTable <- data.frame(sampleName = sampleFiles,
+                           fileName = sampleFiles,
+                           condition = condition)


Error in data.frame(sampleName = sampleFiles, fileName = sampleFiles,  : 
  arguments imply differing number of rows: 0, 4

I have checked individual files and they all have same number of rows.

[Aynur]

Hello, Did you get this problem solved? I also want to merge HTSeq files.

Thanks.

[Kevin Blighe]

akashagri19, please see my answer (below). If you want, please also provide more information about the problem that you are receiving, and try to include a fully reproducible example (of the error) so that we can better help you.

[Aynur]

I used the following code on R

library(tidyverse)
counts_files_pattern = "\\.counts\\.txt$"
counts_table <-
  list.files(pattern = counts_files_pattern) %>%
  #apply an import function to the listed files
  map(function(x) { 
        print(x)
        read_table2(x,
                #rename second column in accordance with the file name
                col_names = c("ID", x))
      }
      ) %>%
  #merge all tables into one
  reduce(left_join, by = "ID") %>% 
  # clean up column names
  rename_all(gsub,
             pattern = counts_files_pattern,
             replacement = '') %>%
  #move ID column to row names
  column_to_rownames("ID")

I have my .txt file on the working directory, but I received this error message

Error: .x is empty, and no .init supplied.

Thanks.

[Ram]

Where did you get this code from? Did you test it step by step?

Answer 1

[Kevin Blighe]

A tip so that you can get through this problem: check the output of each command and be 100% confident that each is producing what you expect.

In your specific example, check what sampleFiles and condition contain. The error message implies that 1 of these variables is empty.

Kevin

[Aynur]

I am sorry; I did not know it is considered as hijacking the discussion. I thought as it is a related question, if we get a solution it might be of help to us.

[Ram]

Please do not do this - you have already opened a question; bugging people on other questions and hijacking those discussions is bad behavior.