not-package/notes/work-plan.md

In eriqande/SNPcontam: Detecting contaminated samples from SNP genotypes

title: "Contaminated SNP Work Plan" author: "Elena Venable and Eric Anderson" output: html_document: toc: true theme: united pdf_document: toc: true

1. Literature Review

• Search for previous research on identifying contaminated samples
• Explore research focused on dealing with non-ideal samples (fecal matter, hair samples, etc.)

2. Likelihood Ratio Test

Question

How much better is the likelihood ratio test than using heterozygousity to determine contaminiation?

Method

Develop Ratio Test

• $\Lambda= log(\frac{p(\theta|con)}{p(\theta | noncon)})$

Develop Heterozygosity Test

Comparison

• Use a Receiver Operator Characteristic curve (ROC) to find the Area Under the Curve (AUC) of the two different methods.
• The better test will have a greater AUC

3. Lab Work and Familiarity

• Become familiar with scoring DNA and recording results

4. Design Lab Experiment

• Design Experiment with Anthony to explore relationship between contamination, amount of DNA, etc.

5. Run Experiment

• Once experiment is designed and decided that it is worth doing, titrate some plates of DNA.

6. MCMC to Determine Allele Frequency in Contaminated Samples

7. Presentation of Results

eriqande/SNPcontam documentation built on May 16, 2019, 8:44 a.m.