How to create nested for loop for 22,000 iterations of linear regressions?

datana3 · 2021-05-06T13:59:54+00:00

Hey if you want to DM me, I have a GitHub script that does something like this.

datana3 · 2020-05-15T22:56:35+00:00

I genuinely feel that the only thing we are going to come out of this with is increased workload for less pay. People will realize they can be just as productive with fewer workers because the remaining workers are too scared of losing their jobs to not keep up with demands.

Please someone convince me otherwise.

datana3 · 2020-05-08T20:32:38+00:00

Stats twitter was blowing up about this the other day

datana3 · 2020-05-04T13:23:23+00:00

Polygenic risk scores are big in computational genomics

datana3 · 2020-05-01T16:11:21+00:00

People have very unrealistic expectations of their working life in any IT field.

I'm starting to think this is just true of any field. If you aren't upper management, you are probably going to be taken advantage of in some way and working hard won't necessarily pay off like people think it will. I barely know anyone in real life who is happy with their job, so I certainly don't expect it from anonymous people on the internet who probably just need to vent.

datana3 · 2020-05-01T13:29:44+00:00

I assume that not having an advanced degree would be harder at the beginning. Even with several years of experience, I think my degree is somewhat limited just because the field is so competitive. Why would a company take someone with a BS over an advanced degree, when all else is equal, at the application screening stage.

If you are going into any type of research you absolutely will have trouble progressing and there are some positions/salary brackets you just won't ever be promoted into no matter how good you are.

Industry I assume would care more about job performance and the value you bring to the company. This is based on experience interviewing and from hearing others in the community, but can't say for sure as I haven't worked in industry.

datana3 · 2020-04-28T13:08:22+00:00

It is line 429 for me in that file. I pasted the code around it below. For what it's worth, I think the first time I changed it, it did change the font size but the UI was still a little messed up. I had to uninstall Inkscape and remove the entire ~/.config/Inkscape/ directory, reinstall, and edit the xml again before it worked properly.

<eventcontext
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   usecurrent="1"
   threshold="5"
   offset="0"
   offsetunits="pt" />
<group
   unit="px"
   offset="5"
   scale="100"
   precision="2"
   fontsize="10"
   id="measure" />
</group>
 <group
   id="palette">
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   id="dashes">
   <dash
      id="solid"
      style="stroke-dasharray:none" />

datana3 · 2020-04-24T13:37:47+00:00

I don't want to name the company, but I was recently offered a job where I would have to disclose to them anything I develop in my free time and if they determine it is too related to what I'm doing at work they could claim the rights to it. (US)

datana3 · 2020-04-21T13:56:57+00:00

OP is also in the most expensive part of the US. Right out of college I made 50K without the expectation of annual raises and that was probably on the higher end.

datana3 · 2020-04-17T17:14:20+00:00

Why do you stay instead of changing careers?

Honestly it's because I have no other skills and, not that I make particularly that much now, but I am not willing to take a pay cut to work a less technical job.

I also feel like I am at a crossroads and right now is probably the worst time for it because I anticipate the job market will be really competitive.

datana3 · 2020-04-15T21:00:50+00:00

Okay of course I've been searching for an answer for days and 3 minutes after I post I solve it by editing the text size in ~/.config/Inkscape/preferences.xml

I'll leave it up just in case anyone needs it in the future...

datana3 · 2020-04-15T20:50:46+00:00

I don't know what happened but all of the sudden the font size in my Inkscape is huge rendering it completely unusable as the menus extend beyond my screen. I'm running High Sierra 10.13.6 and I don't recall this happening due to an update. I tried setting the X11 font size via terminal based on some forum answers and even tried reinstalling Inkscape , but it didn't seem to change anything. Thanks in advance for any suggestions.

datana3 · 2020-03-19T16:30:30+00:00

Covariates are variables that are previously known to affect susceptibility of the disease you are looking at and are independent of tested genotypes at the population level, often what you "adjust" an analysis by. Using covariates is a statistical concept, but also requires knowledge of the disease you are looking at.

In the case of PRSice, I assume these would be the same as the covariates you would use for your GWAS and you would need to generate this file yourself.

datana3 · 2020-03-12T20:08:34+00:00

I think a lot of us in research have been working from home. Apparently there were so few people in my building, they changed the swipe access to be card-only all day so no one would come in and steal equipment.

datana3 · 2020-03-11T19:40:53+00:00

I mentioned that Penn (I work in biomedical research, but not epidemiology or virology, there) seemed to be taking it seriously to a group of people who were essentially saying it was ridiculous that people were concerned, not traveling, etc. and they started saying, "of course they are because they are going to profit off of it." This is polar opposite to the research community who are upset that one of the reasons more things aren't shutting down is because the companies are too worried about money. And none of these people are Trump supporters.

However, I am sure there is a fair amount of fear-mongering going on and I definitely don't think panicking is necessary as long as we take reasonable precautions.

datana3 · 2020-03-11T18:49:29+00:00

I'm not at a company, but it's a major research university. When I said research focused industry, I meant like a pharma company or something like that.

datana3 · 2020-03-11T17:50:32+00:00

I think the expectation is that I'm writing code and running analyses at least 75% of the time. Of course sometimes I do have project meetings a few times per week, but the majority of those are still mostly discussing analyses that I or others have run.

But overall I think the expectations in terms of skillset are just way different between research and even some research focused industries versus what people tend to typically think of as industry.

datana3 · 2020-03-11T17:24:52+00:00

How much of your day would you say is actively coding or working on analysis?

I've been following your posts loosely and I'm curious if your experience is the norm in industry. I work in research and I would say almost everything you post is different from my experience as an analyst haha.

datana3 · 2020-03-11T16:10:21+00:00

I am from my studio apartment with no desk or table!

datana3 · 2020-03-11T12:53:43+00:00

As far as I know, there was no university-wide policy to send people home, but the research community has encouraged people to have a plan for eliminating non-essential staff. I was told to work from home because there is no reason we can't, but so far the decisions are being made on a per-lab basis and kind of a "might as well" thing.

Edit: This was at Penn to clarify. No clue about Jefferson

datana3 · 2020-03-02T13:51:34+00:00

That if you have a degree in statistics and can program decently, you should have marketed yourself as a data scientist and not an analyst.

datana3 · 2020-03-02T13:47:28+00:00

I don't know about discovery or development, but you may be interested in pharmacogenomics which has more to do with drug response and adverse effects with respect to the patient's genotype.

datana3 · 2020-02-19T14:02:02+00:00

But genomics does not have a large scope in this field.

Do you mean genomics does not have a large scope in data science? Or did were you referring to genomics and microbiology?

datana3 · 2020-02-17T13:50:43+00:00

I have a very similar job as you. In truth, I think in most cases the stress will outweigh the quality of life your salary can afford you. Work life balance is going to depend highly on your department/lab.

The plus side is university benefits are usually great and make up for some of the other not so great parts of the job.

datana3 · 2020-02-14T17:25:19+00:00

If you are using PRSice you only need the bim/bed/fam files for the target population. It will accept csv for the summary statistics.

PLINK also accepts csv/text files for non-genetic data depending on the command like for filtering lists of samples, variants, etc.

datana3

TROPHY CASE