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4. Import your data files into R

4. Import your data files into R

Owned by Vicki Thomson
Last updated: Sept 04, 2024
2 min read

To import your data files into R:

In this section, we will import your count table and samples table into R.

You’ll need to change the ‘setwd' line to your working directory. Click ‘Session’ → ‘Set working directory’ → ‘Choose working directory’ and then choose the analysis workshop directory you created previously that contains your R script file and the 'Data’ directory.

 

#### 4. Import your count data #### # Make sure you have: a) your count table (salmon.merged.gene_counts.tsv file, if you used Nextflow nfcore/rnaseq to analyse your data). Copy this to a subdirectory called 'data'. b) your metadata file. This should be either an Excel file called 'metadata.xlsx' or a tab-separated text file called 'metadata.txt'. It needs 3 columns called 'sample_name', 'sample_ID' and 'group'. The sample names should be EXACTLY the same as the names in the count table. These names are often uninformative and long, so the 'sample_ID' is the sample labels you want to put on your plots. E.g. if you have a 'high fat' group, you might want to rename the samples HF1, HF2, HF3, etc) ## USER INPUT # Set working directory. # Change this to your working directory (In the RStudio menu: Session -> Set working directory -> Choose working directory) setwd("H:/workshop/RNAseq/DE_analysis_workshop") # Import your count data. make sure you've created a 'data' subdirectory and put the count table file there. metacountdata <- read.table("./data/salmon.merged.gene_counts.tsv", header = TRUE, row.names = 1) # Import metadata. Again, need a metadata.xlsx file in the data subdirectory. meta <- read_excel("./data/metadata.xlsx") # Remove 1st columns of metadata (gene_name) counts <- metacountdata[ ,2:ncol(metacountdata)] # Rename sample names to new sample IDs counts <- counts[as.character(meta$sample_name)] colnames(counts) <- meta$sample_ID # Counts need to be rounded to integers counts <- ceiling(counts)