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r_test [2020/01/30 17:36]
admin [Question 1]
r_test [2020/03/27 18:46] (current)
admin [Question 2:]
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-**B)** Let's define the //impact// of a set of genes to be the p-value of a log-rank test with the null hypothesis that when all of these genes are mutated ​together, the survival does not change. Write a function ''​most.impact()''​ that takes as input two ''​k1''​ and ''​n1''​ integers, and in the list of ''​n1''​ most mutated genes, finds the names of the ''​k1''​ genes with the best impact. Your function should return the names of the best ''​k1''​ genes (i.e., the set of genes with the best log-rank p-value), and also their impact. Run your function for ''​k1=3'',​ and ''​n1=3'',​ ''​10'',​ and ''​100''​. What is the biological interpretation of your results?+**B)** Let's define the //impact// of a set of genes to be the p-value of a log-rank test that determines whether that gene set is associated ​with survival. Specifically, ​the null hypothesis ​of the log-rank test is that when all of these genes __are mutated ​together__, the survival does not change. ​I.e., we compare the cases who have mutations in all of these genes with the the rest of cases to compute a p-value. A small p-value indicates a significant difference between the two survival curves (KM plots) corresponding to these two groups.\\ 
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 +Write a function ''​most.impact()''​ that takes as input two ''​k1''​ and ''​n1''​ integers, and in the list of ''​n1''​ most mutated genes, finds the names of the ''​k1''​ genes with the best impact. Your function should return the names of the best ''​k1''​ genes (i.e., the set of genes with the best log-rank p-value), and also their impact. Run your function for ''​k1=3'',​ and ''​n1=3'',​ ''​10'',​ and ''​100''​. What is the biological interpretation of your results?
  
 __Hint:__ Use the ''​utils::​c?​m?​n()''​ function, where you need to guess the question marks. __Hint:__ Use the ''​utils::​c?​m?​n()''​ function, where you need to guess the question marks.