Repository for BCB546 R Homework created by Sarah Phelps
A Quarto document was used to create an HTML for the assignment. The documents are named "SP_HW". 40 files have ben created for the teosinte data and the maize data. These files were made from manipulating the snp_position.txt and fan_et_al_genotypes.txt files.
The 10 files named maize1.csv - maize10.csv are seperate files from the maize data for each chromosome in ascending position order.
The 10 files named dmaize1.csv - dmaize10.csv are seperate files from the maize data for each chromosome in descending position order.
10 files named teos1.csv - teos10.csv are seperate files from the teosinte data for each chromosome in ascending position order.
10 files named dteos1.csv - dteos10.csv are seperate files from the teosinte data for each chromosome in descending position order.
Changes to the "SP_HW" quarto document were made from Russell Greene's review. With his comments, I was able to create a loop to more efficently create the 40 data files. His comments are included in this repository.
Visualization plots are included in the html document. These vizualizations include number of SNPS per chromosome, SNP types both teosinte and maize data files, and a comparison of the total number of teosinte and maize samples.
Finally, I've included the 2 review files I created for 2 other students.