Perform enrichment analysis using a hyper-geometric test

Assignment Help Data Structure & Algorithms
Reference no: EM133343390

The attached dataset contains gene expression data for 200 genes for 100 indi-viduals. The first row of the dataset is the phenotype for each individual. Each consecutive set of 10 genes compose a pathway (eg: genes 21 ~ 30 are a pathway). You should code your own function to compute the following tests based on the mathematical basis and algorithm discussed in class. Basic packages are allowed to help with your computation. You could use existing function calls in sklearn, scipy, etc. to check the results of your own function.

Question 1. Estimate the mutual information between each transcript individually and the class label. Print the indices of the 10 transcripts with the highest mutual information with respect to the class label.

Question 2. Use a permutation test to compute top genes that are highly correlated with class label. Permute the class label for 1000 times. Please use Bonferroni correction and BH correction respectively with significance level α = 0.05 and q = 0.1. Please print the output of the identified significant genes for these two corrections respectively. How do they compare?

Question 3. Perform enrichment analysis using a hyper-geometric test on your set of 25 genes and each of the 20 pathways. Determine the 3 pathways for which the set is most enriched. Return the index of that pathway(a number between 1 and 20), as well as the p-value for the enrichment analysis.

Reference no: EM133343390

Questions Cloud

Evidence based practice and Quality improvement : Define and discuss the relationship between Research, Evidence based practice and Quality improvement giving a case scenario related to nursing
What are your current goals as a pmhnp : Review your initial self-reflection for the course. Did you meet your personal goals? What are your current goals as a PMHNP? Have your goals changed
Which are potential effects of substance abuse : Which are the potential effects of substance abuse? A nurse is caring for a group of clients that need assistance. W
Consider that you are a healthcare consumer newly diagnosed : Consider that you are a healthcare consumer newly diagnosed with a serious health problem (select a health concern of interest to you). Assume that you know
Perform enrichment analysis using a hyper-geometric test : Estimate the mutual information between each transcript individually and the class label. Print the indices of the 10 transcripts with the highest mutual inform
Develop criteria to evaluate the effectiveness of the plan : Develop criteria to evaluate the effectiveness of the plan and include a timeline for your change proposal. Finally, reflect on how your change affects
Define the term diversity : Define the term "diversity" and discuss what aspects of Aboriginal and/or Torres Strait Islander culture are diverse.
How can the success of what that nurse can do be measured : How can one nurse help with over crowding of psychiatric emergency rooms/hospitals? How can the success of what that nurse can do be measured?
Describe strategies to address disclosure and nondisclosure : Explain the ethical and legal implications of the scenario you selected on all stakeholders involved, such as the prescriber, pharmacist, patient, and patient

Reviews

Write a Review

Data Structure & Algorithms Questions & Answers

  Implement an open hash table

In this programming assignment you will implement an open hash table and compare the performance of four hash functions using various prime table sizes.

  Use a search tree to find the solution

Explain how will use a search tree to find the solution.

  How to access virtualised applications through unicore

How to access virtualised applications through UNICORE

  Recursive tree algorithms

Write a recursive function to determine if a binary tree is a binary search tree.

  Determine the mean salary as well as the number of salaries

Determine the mean salary as well as the number of salaries.

  Currency conversion development

Currency Conversion Development

  Cloud computing assignment

WSDL service that receives a request for a stock market quote and returns the quote

  Design a gui and implement tic tac toe game in java

Design a GUI and implement Tic Tac Toe game in java

  Recursive implementation of euclids algorithm

Write a recursive implementation of Euclid's algorithm for finding the greatest common divisor (GCD) of two integers

  Data structures for a single algorithm

Data structures for a single algorithm

  Write the selection sort algorithm

Write the selection sort algorithm

  Design of sample and hold amplifiers for 100 msps by using n

The report is divided into four main parts. The introduction about sample, hold amplifier and design, bootstrap switch design followed by simulation results.

Free Assignment Quote

Assured A++ Grade

Get guaranteed satisfaction & time on delivery in every assignment order you paid with us! We ensure premium quality solution document along with free turntin report!

All rights reserved! Copyrights ©2019-2020 ExpertsMind IT Educational Pvt Ltd