The file used in this assignment is the onecombining clinical data and genetic data provided in two previous modules (BRCAMerged.csv). A number of functions have been provided in cells#1-15 of the...

The file used in this assignment is the onecombining clinical data and genetic data provided in two previous modules (BRCAMerged.csv).

A number of functions have been provided in cells#1-15 of the attached notebook (AssignmentWeek6.pdf). The corresponding script is provided as a Jupyternotebook and an R script, both called AssignmentWeek6.

The question asked in this assignment is to compare clustering of this dataset and to map selected genes to biological pathways, in a manner similar to the worksheet.

1) Download the attached files and place them in the same folder:

• BRCAMerged.csv


• AssignmentWeek6.ipynb


• AssignmentWeek6.R

2) Run the script either as AssignmentWeek6.iptnb(Jupyternotebook installation) or as AssignmentWeek6.R (RStudioinstallation).

3) Add the scripts in cells #8 to #19, by taking inspiratin from the corresponding scripts from the worksheet:

• Cell #8select features by running bsswss between the two classes cancer / normal and keep 150 top ranked features in mrnaDataReduced


• Cell #9cluster mrnaDataReduced into 2 clusters with KMeans


• Cell #10display a table showing how the two classes are clustered in the two clusters


• Cell #11plot the two clusters


• Cell #12cluster mrnaDataReduced into 2 clusters with PAM


• Cell #13display a table showing how the two classes are clustered in the two clusters


• Cell #14plot the two clusters


• Cell #15performe gene set enrichment on the 22 top ranked genes Note: because the gene sames are separated by a period instead of |, two of the lines in this cell need to be changed:
  hugoNames
  
  # extract HUGO names
  entrezNames
  
  # extract Entrez names


• Cell #16display a bar plot of the pathways selected


• Cell #17display a gene concept network with cnetplot


• Cell #18display a gene concept network with cnetplot and circular format


• Cell #19display an enrichment map

4) Turn in the assignment as a plain R script file (not Jupyter Notebook file), attached to your submission.

Note: the file BRCAMerged.csv can also be downloaded from Google Drive:https://drive.google.com/file/d/1I8yySge8gTfKR2WlpQ_Q1SSAR-O8dtwn/view?usp=sharing(Links to an external site.)

Attachments

• BRCAMerged.csv:https://drive.google.com/file/d/1I8yySge8gTfKR2WlpQ_Q1SSAR-O8dtwn/view?usp=sharing(Links to an external site.)
  


• 
  AssignmentWeek6.pdf
  


• 
  AssignmentWeek6.ipynb
  


• 
  AssignmentWeek6.r