The file used in this assignment is the one from the worksheet, containing copy number scores for genes(BRCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt).
The attached notebook extracts the group category from the dataset and adds it as a column (AssignmentWeek5.pdf). The corresponding script is provided as a Jupyternotebook and an R script, both called AssignmentWeek5.
There are three major sample groups: primary tumor, metastasis, and normal (normalsamplestaken from the same patients).
1) Download the attached files and place them in the same folder:
- BRCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
- AssignmentWeek5.ipynb
- AssignmentWeek5.R
2) Run the script either as AssignmentWeek5.iptnb(Jupyternotebook installation) or as AssignmentWeek5.R (RStudioinstallation).
3) Create at the end additional code to calculate copy number variations for normal group and for metastasis group. The cells have been prepared but are empty (cells #10-17)
4) Conclude whether you see a pattern by comparing copy number variations between the three groups: primary tumor, normal, and metastasis.
5) Turn in the assignment as a plain R script file (not Jupyter notebook file), attached to your submission.