HW1: Sequencing, Statistical Concepts, and Population Genetics Solution

1    Sequencing and Assembly

    1. What is shotgun sequencing and how has this technique significantly contributed to the acquisition of the human genome?

    2. What are the relative advantages and disadvantages of Sanger sequencing vs. next generation (Illumina) sequencing?

    3. What is paired-end sequencing? Give a cartoon example (i.e., a sample set of reads and/or a piece of a genome) where paired-end sequencing leads to improved assemblies.

    • Computing q-values from p-values

Here we’re going to analyze a file that contains a table with two columns:

pval: p-values from simulated data (t-test on counts from Poisson model with random values; details aren’t important).

null: has a value of 1 if the p-value is for a condition-negative case (where the null hypothesis holds) or 0 otherwise (the alternative hypothesis holds).

Note the second column has information that would be unknown in practice, but we’ll use it in this thought experiment to understand how q-value estimation works. Write an R script that does the following:

    1. Load the file sim-pvals.txt. Hint: use the R function read.table, though other functions can be used too.

    2. What is  0 (the proportion of condition-negatives or null hypotheses) in this data?

    3. Plot the p-value distribution of the null and alternative p-values separately. Hint: use the R function hist. Why do these distributions have the observed shapes?

    4. Now plot the combined p-value distribution. Please use the freq=FALSE option if you’re using hist, so the y-axis shows the density rather than the frequency of each bin. Draw a horizontal line with a height of 0 on this density. What does 0 correspond to in this figure?

    5. Based on the last figure, how do you suggest estimating 0 from the combined p-value distribution when the true condition of each case is unknown? No equations are necessary, a one-sentence summary of most important part of the strategy suffices.

    6. Calculate q-values manually:

For each p-value p, start by using this formula that estimates the FDR:
q0(p) =   pm 0   ;

#fp0    pg

where m is the number of p-values, 0 is the true value of the parameter you calculated earlier from the null column, and #fp0 pg is the number of p-values in the whole list that are smaller or equal to the given p.

The next step is to ensure monotonicity. Typically the FDR increases as the p-value increase. When the FDR estimate actually get smaller for a larger p-value, you should accept the lowest FDR you can that includes your given p-value: q(p) = minp0 p q0(p0)
Lastly, cap q-value estimates to 1 as needed.

    7. Explain why q0(p) above estimates the FDR. In particular, explain what #fp0 pg is, what pm 0 estimates, and why their ratio estimates the FDR.

    8. Plot q-values against p-values and describe the relationship. What is the maximum q-value and why?

    9. Compute q-values with the R qvalue package.

    (a) If you are programming in R, install the R qvalue package. To do this you need to use BiocManager from bioconductor by running the following in the R console:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("qvalue")

If you run into any problems this might mean you a version of R < 3.5 (double check by typing version in the R console), then type the following in the R console:
 source("https://bioconductor.org/biocLite.R")

biocLite("qvalue")

To compute q-values with the package, use the function qvalue of that same package.

    (b) If you are programming in another language, you can use the qvalue web server instead (http://qvalue.princeton.edu/). Upload the sim-pvals.txt file and change the "Separator" option to "Tab." Output > Summary will show the results and estimates of the run, and if you scroll to the bottom, the "Download Output" button will give you a data file you can import for plotting.

Use the original p-values and nothing else as input, with default options. Report the 0 estimate of the package.

    10. Show a plot that compares our manual q-value estimates with the q-value estimates of the package, and the y = x line for comparison. Do they differ? Why?



































    •  Precision-recall Analysis

For this problem, you will need to examine a ranked list of genes and determine whether or not the ranking is biologically relevant. Specifically, you will ask whether genes, known to be associated with a particular biological function, preferentially occur at the top of your experimental list or, alternatively, are randomly scattered throughout the list.

Imagine that you have performed an experiment in which you have treated yeast Saccharomyces cerevisiae with a chemical compound. To determine which yeast genes are likely responsible for protecting the cell against chemical stress, you have measured the expression of all genes before and after the treatment. After performing proper corrections and normalizations, you came up with a list of genes that are differentially expressed upon treatment and ranked the genes based on the extent and confidence of their differential expression.

3.1    Data import and cross-checks

To work on this problem you will need to download the following datasets and import them into your working environment. The R function read.table might be useful here, although definitely not the only way to import your data.

    1. The list of genes that are differentially expressed in your experiment: differentially_expressed_orfs.txt

    2. The list of genes known to be involved in a specific biological process: positive_orfs.txt

To verify that your data import was successful, perform the following cross-checks:

    1. Is your list of differentially expressed genes unique? If not, which genes are repeated? How many times are they repeated? Remove the repeated ORFs, if any, keeping only their first occurrence. Hint: the R functions length, unique, and table might be useful.

    2. How long is the list of known genes? How many of them appear in your differentially expressed list?

3.2    Precision-recall analysis

Assume that the order of genes in the differentially_expressed_orfs.txt file reflects their experimental ranking, which is based on the extent and confidence of their differential expression. At each position in this ranked list, calculate the precision and the recall of the data relative to the list of known genes. Plot the corresponding precision-recall plot. Assume that every gene in the genome was tested for differential expression, even those that do not appear in the list of differentially-expressed genes.

    1. What is the precision of these data at 10% recall?

    2. Do you think it is reasonable to conclude that your experiment is recapitulating well previously known biology? Motivate your answer.

















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    • Population Genetics

The files pop1.txt and pop2.txt contain genetic data from a 10 kb region sequenced in two populations. Each biallelic segregating site (S) contains two alleles, labeled 0 or 1. For each population, genetic data from 100 chromosomes was obtained, where each line represents genetic data from a different chromosome (another way to describe the data is that each line represents a different haplotype; alleles at loci that occur on the same chromosome). For example, "0100" means there are four segregating sites in this region and this particular chromosome has allele 0 at the first segregating site, allele 1 at the second segregating site, allele 0 at the third segregating site, and allele 0 at the fourth segregating site.

    1. Write code to determine the number of segregating sites, S, in populations 1 and 2. Hint: the R function readLines can help read in the data files.

    2. For each population, calculate a per nucleotide estimate of W and (i.e., divide W and by the number of bps sequenced in the region).

3. Calculate the statistic D =    W for each population.

    4. Use your estimates of W to estimate Ne in each population. Note that for this problem, you can assume that the mutation rate is equal to 1 10 8 per site per generation.

    5. Based on the data in 1-4, do you think Ne is the same or different between population’s 1 and 2? What aspects of the data are most informative in arriving at your answer?









































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