homework07

MCB536 Homework 7

This assignment is due on Nov 30, 2023.

Total: 50 points

Complete this homework by writing R code to complete the following tasks. Please use the R Markdown file provided to you homework07.Rmd.

i. Empty chunks have been included where code is required.
ii. For Problem 2c, you should include a image (screen shot) instead of providing code.
iii. This homework requires use of

• BRCA.genome_wide_snp_6_broad_Level_3_scna.seg (Problems 1, 2)
• BRCA_IDC_cfDNA.bam and "BRCA_IDC_cfDNA.bai (Problem 3)
• GIAB_highconf_v.3.3.2.vcf.gz (Problem 4)

iv. You will be graded on your code and output results (Rmd file and knitted html/pdf file). Partial credit may be given for all questions.

When you are satisfied with your code and answers, use the "Knit" button in RStudio to create the final set of files that you will submit for grading.