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Empowering RNA-Seq Analysis: Building and Utilizing Your Custom R Package

  Introduction In the vast realm of bioinformatics, understanding gene expression is crucial for unraveling the mysteries of biology and disease. One powerful tool in this pursuit is the R programming language, enriched by packages like DESeq2 for conducting differential gene expression analysis. However, navigating these tools can be complex for beginners. That's where our custom package, MyDataAnalytics, steps in to streamline the process. In this blog post, we'll walk you through the steps of conducting differential gene expression analysis using MyDataAnalytics, simplifying a task that can often seem daunting. Part 1: Creating Your Custom R Package Creating a custom R package involves several steps, from defining functions to structuring directories and documentation. Let's outline the process: Define Functions : Begin by defining functions that encapsulate specific tasks related to RNA-Seq analysis, such as creating DESeqDataSet objects, running DESeq analysis, filteri...
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Exploring Input/Output, String Manipulation, and plyr Package in R: A Step-by-Step Guide

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Hello all, In our latest blog post, we'll delve into some important principles of R programming. These include Input/Output operations, string manipulation, and using the plyr package for data manipulation. We'll be following a structured approach outlined by Dr. Friedman, and take a step-by-step approach to explore these concepts using a dataset. By doing so, we aim to gain a deeper understanding of these concepts. Step 1: Importing Data and Calculating Means by Category Our first task is to import Assignment 6 dataset into R and calculate the mean grade based on the category of 'Sex' using the plyr package. After importing the data using the read.table() function, we load necessary packages including plyr and perform the mean calculation using ddply(). Finally, we write the resulting output to a file. Step 2: Filtering Data based on Names containing 'i' Next, we convert the dataset into a dataframe and filter it to include only the rows where the student names...
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My intro to R programming

 Hey everyone! I just tested a function for calculating the mean using R studio, and I'm excited to share the results with you! Please refer to my   GitHub repository  for my work. After applying the function to my dataset (assignment), the mean value is 19.25.  I followed the instructions given by my professor Dr. Friedman and referred the book "The Art of R Programming" by Norman Matloff. Explanation: This function works by summing up all the values in the given dataset (sum(assignment)) and then dividing the sum by the total number of elements in the dataset (length(assignment)) , it calculates the average value of the dataset. The formula for mean is: Mean = Sum of Values / No. of Values In this case, the function successfully computes the mean of the 'assignment' dataset. Feel free to try it out with your own datasets or explore Matloff's book!                                 ...
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