R Sanity Check

[utsavlamichhane]

File: .github/workflows/r-ci.yml

name: R Sanity Check

Trigger on pushes or pull requests to main (adjust branch names if needed)

on:
push:
branches:
- main
- master
pull_request:
branches:
- main
- master

jobs:
sanity-check:
name: Run R Sanity Check
runs-on: ubuntu-latest

steps:
  #  Check out the repository
  - name: Check out code
    uses: actions/checkout@v3

  # Set up R (adjust r-version if necessary)
  - name: Set up R
    uses: r-lib/actions/setup-r@v2
    with:
      r-version: '4.2'

  #  Install any R packages your script needs
  - name: Install R dependencies
    run: |
      Rscript -e 'install.packages(c("dplyr", "tidyr", "readr"), repos = "https://cloud.r-project.org")'
      # If you need Bioconductor packages, uncomment and adjust lines below:
      # Rscript -e 'if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager")'
      # Rscript -e 'BiocManager::install(c("edgeR", "limma"), ask = FALSE)'

  #  Run a quick sanity-check R script (will fail if example.R errors out)
  - name: Run example.R
    run: |
      Rscript --vanilla Tutorials/example.R

[utsavlamichhane]

#!/usr/bin/env Rscript

Tutorials/example.R

A minimal sanity‐check script that:

1. Verifies “raw_counts.tsv” exists in the repo root.

2. Reads it into a data frame.

3. Prints the dimensions and first few lines.

4. Creates a tiny summary file “sanity_summary.tsv” with the first five genes’ total counts.

Firstly, Check that raw_counts.tsv exists

if (!file.exists("raw_counts.tsv")) {
stop("ERROR: raw_counts.tsv not found in the repository root. Make sure this file is present.")
}

2) Read the raw counts table

- Assumes the first column is a gene identifier and the remaining columns are numeric counts.

counts <- read.delim(
file = "raw_counts.tsv",
header = TRUE,
sep = "\t",
stringsAsFactors = FALSE
)

##3) Print basic info to the console

cat(">>> raw_counts.tsv successfully loaded.\n")
cat("Dimensions: ", nrow(counts), "rows x", ncol(counts), "columns\n\n", sep = " ")
cat("First 5 rows:\n")
print(head(counts, 5))
cat("\n")

4) Build a tiny summary: compute total count per gene, then save the first 5 rows

- Assumes column 1 is “Gene” and the rest are numeric count columns.

summary_df <- data.frame(
Gene = counts[[1]],
TotalCount = rowSums(counts[ , -1 ], na.rm = TRUE),
stringsAsFactors = FALSE
)

Keep only the top 5 rows for brevity

tiny_summary <- head(summary_df, 5)

####Write out the small summary table to sanity_summary.tsv
write.table(
tiny_summary,
file = "sanity_summary.tsv",
sep = "\t",
row.names = FALSE,
quote = FALSE
)

cat(">>> Wrote a tiny summary (first 5 genes) to sanity_summary.tsv\n")