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SubjectR | R Studio
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Short Assignment Requirements

Please submit your final project report as two attachments -1. R Notebook file2. FASTA and GFF files for the organisms analyzed in a single ZIP file.

Assignment Description

Guidelines for Final Lab Report  

Course: 01:447:303

Author: Prof. Premal Shah  

Objective: The primary objective of the finals lab report is to apply R programming skills to perform comparative analyses of genomic features of any two organisms.  


     Overview: Comparative analyses of genomic datasets  

     Submission format: The finals project report will be submitted as a single R HTML Notebook (*.nb.html) file. Any additional files or datasets needed to execute the code can be submitted as a single ZIP file.  

     Structure: The report will contain the following sections  

a.    Title: The authors will create a descriptive title for their report and list the names of all authors.  

b.    Introduction: The authors will justify their choice of organisms and the nature of genomic comparisons. (1—2 paragraphs)  

c.    Code: Before each code chunk the authors will describe what data/ analyses/plot that particular chunk will generate.  

i.      Comments: The R code will be extensively commented. Lack of clear comments will lead to loss of points.  

ii.    Plots: The report will contain 3 plots each describing unique analyses

(see below). iii. Statistical tests: The report will contain the code for statistical analyses. The authors will also justify their choice of a particular statistical test.  

iv. Inferences: The authors will provide descriptive statements indicating what inferences were drawn based on their plot/statistical analyses.  

d. Summary: At the end of the report, the authors will summarize their findings in a summary paragraph.  Examples: 

a.     Compare distribution of gene lengths. Does one organism have longer genes on average than another?  

b.     Compare GC content of genes. Are genes of one organism more GCrich than 

c.     Compare frequency of particular amino acid usage. Is one (or more) amino acid used more frequently in one genome than another?  

d.     While students can use these example analyses for their finals report, extra 
points will be awarded for novel analyses. 

Points: Total 50 points  

     Title — 1 pt  

     Introduction — 5 pt  

     Analyses  —

a.     Each plot — code (3pt) + comment (1pt) + accuracy/aesthetics (1pt) = 15 pt.

b.     Each statistical test — code (3pt) + comment (1pt) + justification (1pt) = 15 pt

c.     Each inference — 3pt = 9 pt  

     Summary — 5 pt 

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