R Programming Journal – Premitha Pagadala

OncoMarker: Targeted Genomic Biomarker Discovery in Breast Cancer Introduction High-throughput sequencing has transformed oncology, producing massive datasets that describe gene expression, mutations, and epigenetic alterations. While this wealth of information has propelled research, whole-genome analyses often overwhelm computational pipelines and slow clinical translation. Cancer research generates massive genomic data, but analyzing all ~20,000 genes is computationally heavy and hard to interpret.  OncoMarker addresses this challenge by providing a streamlined R framework for analyzing targeted gene panels , enabling researchers and clinicians to quickly identify differential expression patterns, visualize results, and stratify patients based on biomarker risk. The package is designed to be accessible, operating on pre-processed expression matrices rather than raw sequencing data. Ideology The philosophy of OncoMarker is simple: "The Simple Twist" . Instead of starting w...

  Assignment 12:  My R Markdown Primer: Bioinformatics Workflow Objectives I explored R Markdown and its capabilities for creating reproducible reports, particularly in bioinformatics . R Markdown allows you to combine narrative text, code, and output in a single document, which is especially useful for RNA-Seq analyses where workflows can be complex and data-intensive. I practiced: Writing narrative text with headings, bullet points, and emphasis. Using inline and displayed LaTeX equations , for example, the Hardy-Weinberg equilibrium : Inline: $p^2 + 2pq + q^2 = 1$ Displayed: p 2 + 2 p q + q 2 = 1 p^2 + 2pq + q^2 = 1 This helped me document mathematical models used in bioinformatics clearly. Integration of Code and Narrative I loaded the airway RNA-Seq dataset from Bioconductor. Converted it into a DESeq2 object and performed variance stabilizing transformation (VST). Conducted PCA analysis to visualize sample clustering. All of this was embedd...

  Assignment 11: Debugging Turkey Outlier Function in R Objectives For this assignment, I debugged an R function called tukey_multiple() that was supposed to identify rows in a numeric matrix whose values are outliers in every column according to the Tukey rule (1.5 × IQR). The function initially contained a deliberate bug involving a logical operator that prevented it from running correctly. The steps included: Reproducing the error. Diagnosing the bug. Fixing the code. Validating the fix. Adding defensive programming checks. Documenting the debugging workflow. R Code Reproduce the Error Error Message Diagnosing the Bug && is a scalar (short-circuit) operator In R, && only evaluates the first element of each vector. Its output is a single TRUE or FALSE, not a vector . outliers[, j] and tukey.outlier(x[, j]) are vectors In the test case, each column has length 10. Using && tries to combine two vectors into a s...

  Assignment 10: Building Your Own R Package Objectives The Premitha package is an R package designed to simplify common data analysis and visualization tasks. It is intended for students, researchers, and analysts who want to quickly explore datasets, summarize numeric variables, and create basic plots without writing repetitive code. R Code # Step 0: Install tools install.packages("devtools") install.packages("roxygen2") library(devtools) library(roxygen2) # Step 1: Create your package setwd("/Users/premithapagadala/Documents/R_Programming_Fall2025_Pagadala_Premitha/Assignments/Assignment_10_Create_Package") create("Premitha") setwd("Premitha") #working directory inside your package # Step 2: Write DESCRIPTION file desc_lines <- ' Package: Premitha Title: Simple Tools for Streamlined Data Analysis Version: 0.0.0.9000 Authors@R:      person("Premitha", "Pagadala",             email = "premithapagadala@g...