Learn to combine data frames when limited to subsets of your overall data.

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There are many valuable tools in R for data science. Recently, I have been using LDLinkR to gather linkage disequilibrium statistics for my research. What I quickly discovered is that this algorithm can only process a maximum of 1,000 SNPs per iteration. Given that data is outputted as a data frame, I am left with several disjointed data frames that I want to combine to form a single data frame required for my pipeline. This can be visualized by the following where I want to combine the smaller squares into a larger square:

Guide to using this helpful genetics tool

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There are many valuable tools for a research scientist in genetics. One such tool is the Integrative Genomics Viewer. This program has several functions useful for someone looking at sequencing data. I will be going over a focused function for one seeking to grab select data quickly.

Homozygous or Heterozygous?

Heterozygosity has implications on physical traits and the strength of a harmful effect. Inspecting for this is fortunately relatively easy. After loading a genome file, zoom into your desired locus by entering the locus into the bar at the top of the screen:

A brief recount of my post-vaccine experience.

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It has been unfortunate that there has been so much misinformation about the life-saving COVID-19 vaccines. The vaccine is the best way to prevent death from COVID-19, a genuine possibility (at least 5 people in 100) if one gets infected and is not vaccinated. Overall, its side effects are minimal and reasonable, considering that it prevents me from dying from the virus. This is a brief recount of my experience receiving my second vaccine. I am fully transparent with the side effects that I experienced.

When I went to the vaccine distribution site with my wife, there was not much…

A brief statement on why there is little to gain from protesting COVID-19 restrictions.

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I recently read an article from the Montreal Gazette documenting protests against COVID-19 restrictions, including a curfew. Comments raised beliefs that not wearing masks and obeying restrictions was an act of courage and exercising freedoms. Below is the statement that I made about such actions.

MD and COVID-19 researcher here. I’m afraid I have to disagree with commenters suggesting that a refusal to wear masks and obey restrictions is a ‘courageous exercise of freedom.’ The pandemic has gone on for over a year. Millions have gotten sick and died, which included many in the United States who were exercising such…

Summary of where we are with COVID.

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It feels like COVID-19 has been going on for a long time because it has, and the inconveniences become increasingly annoying every day. Fortunately, a greater proportion of the international population is vaccinated, and more progress is being made towards herd immunity. I summarize here points that I have made while fighting COVID misinformation online, given that these are thus the questions that most concern us at this point.

Does the vaccine protect me against the new variants?

The vaccine still has effectiveness against the new variants. True, you can still be infected while vaccinated, but being vaccinated prevents you…

When claims of freedom blind us of their potentially insular nature

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Protests against COVID-19 policies have persisted throughout the pandemic. I can understand wanting life to be back to normal, visiting friends and family, and doing something as basic as going to a restaurant with my wife. As a physician, I am disturbed that such protests often perpetuate falsehoods about the pandemic, such as it not being real, it being no worse than the flu, and the number of dead is inflated or similar compared to other years. I find the last the most egregious as it suggests that all of those we have lost did not matter.

I have been…

I describe the twenty-four hours following my COVID-19 vaccine.

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There is a lot of misinformation regarding COVID-19 vaccines. I have written multiple articles on my Medium page documenting the objective aspects of COVID-19, including vaccine side effects. Yesterday, I was fortunate to receive my COVID-19 vaccine as some researchers had the opportunity to sign up for it.

I flowed through the registration at the vaccination center relatively quickly. As with every other medical procedure, I was appropriately asked for contraindications to the vaccine (have I had reactions to vaccines in the past). The center exists so people who have severe reactions can be cared for (a stretcher in a…

The vaccines are no longer experimental. They have "passed" and are now approved for general use. Being approved under emergency legislation does not mean safety assessments were skipped or minimized. Providers also have the ethical responsibility of "justice," which means here to ensure public health in this public health crisis. Receiving a vaccine (and being mandated to given no medical contraindications, even though it is a hard line), is essential for patient safety as a provider can be infected without knowing it, masks are not perfect, and hospitalized patients are more likely to suffer and die if they get COVID…

Review of this generally accessible textbook

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As I have been occupied with my research, textbooks have been a more frequent companion than Medium as I have been seeking to improve my knowledge to do better work. Given my recent desire to choose ideal sampling periods for data analysis, I read through the book Essentials of Epidemiology in Public Health by Ann Aschengrau and George R. Seage III, 2020. Both of the authors are public health specialists and thus well-suited to contribute to this textbook.

As one with a stronger background in epidemiology and public health, this book was less useful because it mainly focused on the…

I apologize for my recent paucity of articles. My COVID-19 research has become even more demanding than before and I am investing my time into contributing to the science that…

Julian Willett, MD

Loving husband. Physician scientist who enjoys spreading his knowledge with the world whether related to medicine, technology, or science.

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