mixer | Causal Mixture Model for GWAS summary statistics

 by   precimed C Version: v1.2 License: GPL-3.0

kandi X-RAY | mixer Summary

kandi X-RAY | mixer Summary

mixer is a C library. mixer has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

This folder contains a Python port of MiXeR, wrapping the same C/C++ core as we previously used from MATLAB. This is work in progress, but eventually it should singificantly improve user experience, as Python allows much simpler installation procedures, makes it less error prone, allows to implement well-documented command-line interface (python mixer.py --help), and provide visualization. Input data for MiXeR consists of summary statistics from a GWAS, and a reference panel. MiXeR format for summary statistics is compatible with LD Score Regression (i.e. the sumstats.gz files), and for those users who are already familiar with munge_sumstats.py script we recommend to use LD Score Regression pipeline to prepare summary statistics. At the same time, we encourage everyone to take a look our own pipeline for processing summary statistics. For the reference panel we recommend to use 1000 Genomes Phase3 data, pre-processed according to LD Score Regression pipeline, and available for download from LDSC website. Further details are given in Data downloads and Data preparation sections. Once you have all input data in MiXeR-compatible format you may proceed with running univariate (fit1, test1) and cross-trait (fit2, test2) analyses, as implemented in mixer.py command-line interface. The results will be saved as .json files. To visualize the results we provide a script in python, but we encourage users to write their own scripts that understand the structure of .json files, process the results. Further details are given in Run MiXeR, MiXeR options and Visualize MiXeR results sections. If you encounter an issue, or have further questions, please create a new issue ticket.
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            kandi-support Support

              mixer has a low active ecosystem.
              It has 31 star(s) with 11 fork(s). There are 19 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 28 open issues and 38 have been closed. On average issues are closed in 48 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of mixer is v1.2

            kandi-Quality Quality

              mixer has 0 bugs and 0 code smells.

            kandi-Security Security

              mixer has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              mixer code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              mixer is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              mixer releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            mixer Key Features

            No Key Features are available at this moment for mixer.

            mixer Examples and Code Snippets

            Run MiXeR,Bivariate (cross-trait) analysis
            Cdot img1Lines of Code : 21dot img1License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            python3 /python/mixer.py fit2 \
                  --trait1-file PGC_SCZ_2014_EUR_qc_noMHC.csv.gz \
                  --trait2-file SSGAC_EDU_2018_no23andMe_noMHC.csv.gz \
                  --trait1-params-file PGC_SCZ_2014_EUR_qc_noMHC.fit.rep${SLURM_ARRAY_TASK_ID}.json \
                  --trait  
            Run MiXeR,Univariate analysis
            Cdot img2Lines of Code : 16dot img2License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            python3 /precimed/mixer.py fit1 \
                  --trait1-file SSGAC_EDU_2018_no23andMe_noMHC.csv.gz \
                  --out SSGAC_EDU_2018_no23andMe_noMHC.fit.rep${SLURM_ARRAY_TASK_ID} \
                  --extract LDSR/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p  
            MiXeR options
            Cdot img3Lines of Code : 7dot img3License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            python3 mixer.py ld --help
            python3 mixer.py snps --help
            python3 mixer.py fit1 --help
            python3 mixer.py test1 --help
            python3 mixer.py fit2 --help
            python3 mixer.py test2 --help
            python3 mixer.py perf --help
              

            Community Discussions

            QUESTION

            What to do with many almost-same if-statements?
            Asked 2022-Mar-11 at 05:29

            I need help. Im new on coding, so I've developed a game with pygame. It's a game where you fight as a robot against a zombie. If a fireball collides with the zombie, the heart picture will be updated from filled to half and so on.

            The Tech-Lead said that this code is not efficient because of the many if statements in the def hearts() method in the Enemy class.

            Could you please help me to shorten it? I have absolutely 0 idea what I could do. Thinking about loops, but dont know how to do it. Please help me

            Here is my code:

            ...

            ANSWER

            Answered 2022-Mar-11 at 00:50

            The tech-lead is wrong: your code is perfectly efficient the way it is written. Making the code shorter does not make it faster or more "elegant".

            However, shorter code can be easier to maintain and change. Your code is fine as long as the number of heart containers is always exactly 12. But if you want to change that (to increase/decrease the difficultly of the game, or let the player get new heart containers) then this code won't work. It is hard-coded to work with exactly 12 heart containers only.

            To change this, put this repetitive code in a loop. You'll need to look at the pattern of how the numbers change and create a small math formula for it. I've come up with the following. (I've also added constants instead of the integer literals, so that the code is easier to read and change.)

            Source https://stackoverflow.com/questions/71432303

            QUESTION

            Delete Duplicate records with exact value
            Asked 2022-Feb-14 at 10:18

            How to delete duplicate records when both rows the exact same records?

            ...

            ANSWER

            Answered 2022-Feb-14 at 10:09

            I would actually suggest creating a temporary table, inserting the records sans duplicates, then renaming the temp table to the original table name.

            Source https://stackoverflow.com/questions/71110022

            QUESTION

            How to use muti-language in 'gTTS' for single input line?
            Asked 2022-Jan-29 at 07:05

            I want to convert text to speech from a document where multiple languages are included. When I am trying to do the following code, I fetch problems to record each language clearly. How can I save such type mixer text-audio clearly?

            ...

            ANSWER

            Answered 2022-Jan-29 at 07:05

            It's not enough to use just text to speech, since it can work with one language only.
            To solve this problem we need to detect language for each part of the sentence.
            Then run it through text to speech and append it to our final spoken sentence.
            It would be ideal to use some neural network (there are plenty) to do this categorization for You.
            Just for a sake of proof of concept I used googletrans to detect language for each part of the sentences and gtts to make a mp3 file from it.

            It's not bullet proof, especially with arabic text. googletrans somehow detect different language code, which is not recognized by gtts. For that reason we have to use code_table to pick proper language code that works with gtts.

            Here is working example:

            Source https://stackoverflow.com/questions/70852444

            QUESTION

            remove EventListener from treejs AnimationMixer
            Asked 2022-Jan-07 at 17:05

            I have an AnimationMixer and I wanted to attach some logic to the end of the animation.
            As the documentation instructs - I used addEventListener on the mixer, and it worked fine,
            BUT when I tried to remove the listener it didn't work.
            (I also tried to see if hasEventListener works, but no luck.)

            In short-
            The log for addEventListener is working
            but removeEventListener and hasEventListener do not.
            What am I missing? I could not find any explanations for this.
            Would appreciate any help...

            ...

            ANSWER

            Answered 2022-Jan-07 at 17:05

            RemoveEventListener() accepts a second argument to know which event to remove, but that function doesn’t get triggered on removal. Plus, it should be the same function each time, not a new one:

            Source https://stackoverflow.com/questions/70611505

            QUESTION

            Increasing variables that are in use in pygame
            Asked 2021-Dec-25 at 09:30

            I am coding a space invaders game in pygame, and wanted to make it so that when the player reaches 50 points, the game increases the number of invaders from 6 to 10. In the game, the enemies respawn near the top half of the screen immediately after dying. The game functions perfectly normally until you reach 50 points, at which it immediately crashes. How do I make it so that the variable storing the number of enemies (num_of_enemies) increases, while the game is still running?

            In the code I have put here, I removed my attempt to change the num_of_enemies variable, but fyi, I placed it just above "pygame.display.update()". my crappy attempt to resolve the issue boiled down to:

            if score_value >= 50: num_of_enemies += 10

            I have also tried this code while assigning num_of_enemies a global value, but it simply defects the game, and messes up again.

            Code:

            ...

            ANSWER

            Answered 2021-Dec-25 at 09:30

            IT is not enough just to change num_of_enemies you also need to add new items in the lists.

            Write a function that crates the enemies:

            Source https://stackoverflow.com/questions/70477198

            QUESTION

            How can I Iterate through a list of songs and play them one after eachother
            Asked 2021-Dec-23 at 12:45

            I am looking to iterate through a list of songs such as Songs = ["Song1.mp3", "Song2.mp3", "Song3.mp3"] and I want to play each song one after each other.

            I have tried various methods, the most suggested seemed to use pygame, however, I have not been able to debug the tremendous amount of errors that come with using it. My main source code and attempt at this is as shown below:

            ...

            ANSWER

            Answered 2021-Dec-23 at 05:10

            If it's a desktop app, you have multiple options to play a file, usually, it depends:

            Also to avoid Tkinter being stuck, you need to use threads or multiprocess. I recommend you soundfile player, you will find examples here https://realpython.com/playing-and-recording-sound-python/

            Source https://stackoverflow.com/questions/70457867

            QUESTION

            Is there any way to include all of the sound effects for my pygame game into my .exe with pyinstaller?
            Asked 2021-Nov-28 at 16:30

            I have made a relatively simple pygame program with 9 different sound effects (.wav format, if this information is important). When converting my main.py to an executable file with the pyinstaller module, is there any way I can get the sound effects to be included in the executable, or will I need to find a work-around (such as having the sound effects in the C:\Program Files path)?

            Here's the contents of my .spec file:

            ...

            ANSWER

            Answered 2021-Nov-28 at 16:30

            The pyinstaller documentation states:

            The list of data files is a list of tuples. Each tuple has two values, both of which must be strings:

            • The first string specifies the file or files as they are in this system now.

            • The second specifies the name of the folder to contain the files at run-time.

            That means that if you do this:

            Source https://stackoverflow.com/questions/70134677

            QUESTION

            Why doesn't the 3D model work with AmbientLight?
            Asked 2021-Nov-03 at 08:16

            I add a 3D model in Three.js, but when I turn on AmbientLight, the model doesn't light up as it should. While other 3D models work fine. It's already clear to me that the problem is in the 3D model, but which parameter in textures or in general in the Blender application I broke, I can't understand. It looks like this:

            Code:

            ...

            ANSWER

            Answered 2021-Nov-03 at 08:16

            All materials of your asset have a metalness value of 1. Ambient lights do not affect metallic surfaces.

            Considering the type of your asset (a property), the current material parametrization does not make sense. Not everything on a house is metallic.

            Since you are not using an environment map right now, you should set the metalness property to 0 anyway.

            Source https://stackoverflow.com/questions/69821345

            QUESTION

            How to place functions inside tkinter drop down list?
            Asked 2021-Sep-16 at 03:21

            So, my purpose with this program is to store, whats displayed on the main frame, inside the drop down list, which shows the list of the rappers. So instead of just being displayed on the main frame, I want it to be hidden until the particular name of the artist (to whom the the picture, play button and stop button belongs to) is picked in the list. Please help me with this. Thank you.

            This is the screenshot of the program atm. So far there are 4 things displayed on the main frame The list which was made with tkinter, picture, play button and the stop button.

            ...

            ANSWER

            Answered 2021-Sep-16 at 03:21

            You can create a frame to hold the image and the buttons and this frame is initially hidden.

            Then associate a function on the OptionMenu via command option. The function will be executed whenever option is selected. Inside that function you can load the corresponding image and song based on the selected artist:

            Source https://stackoverflow.com/questions/69201128

            QUESTION

            How to retrieve audio session name similar to one in Windows' built-in mixer app?
            Asked 2021-Sep-03 at 18:29

            I'm building a mixer app and need to get the user-friendly names for each audio session.

            I tried:

            1. IAudioSessionControl::GetDisplayName() method, but it returned empty string for each session.

            2. Calling QueryFullProcessImageName() and GetModuleFileNameEx(), but they only output C:\Users\ since I have Cyrillic letters in the path. But even if they did output the full path, I assume it would end with something like ...\brave.exe (correct me if I'm wrong), which is not a user-friendly name like Brave Browser in Windows' built-in mixer.

            3. I also tried getting all process names and PIDs like this, and later match them to session process IDs, which successfully gave me names like chrome.exe or steam.exe, but they are still, again, not quite what I want:

              ...

            ANSWER

            Answered 2021-Sep-03 at 18:29

            Calling QueryFullProcessImageName() and GetModuleFileNameEx(), but they only output C:\Users\ since I have Cyrillic letters in the path.

            Then you are simply not displaying the path correctly. The presence of Cyrillic characters is not a problem.

            I also tried getting all process names and PIDs like this, and later match them to session process IDs, which successfully gave me names like chrome.exe or steam.exe, but they are still, again, not quite what I want

            That code doesn't work properly. You are storing pointers in your std::vector that point to a single wchar_t[] buffer which is modified on each loop iteration. You should instead store std::wstring instead of wchar_t* so each path is copied.

            What I want is to retrieve names like in the built-in mixer app, ie Steam, Chrome Browser, Zoom Meetings, etc.

            Once you have the path to the EXE, you can use GetFileVersionInfo() and VerQueryValue() to retrieve the app's human-readable FileDescription. See Retrieve File Description for an Application using VerQueryValue.

            Source https://stackoverflow.com/questions/69036476

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install mixer

            The exact steps depend on your build environment.
            If you work in HPC environment with modules system, you can load some existing combination of modules that include Boost libraries: module load CMake/3.15.3-GCCcore-8.3.0 Boost/1.73.0-GCCcore-8.3.0 Python/3.7.4-GCCcore-8.3.0 # TSD (gcc) module load Boost/1.71.0-GCC-8.3.0 Python/3.7.4-GCCcore-8.3.0 CMake/3.12.1 # SAGA (gcc) module load Boost/1.68.0-intel-2018b-Python-3.6.6 Python/3.6.6-intel-2018b CMake/3.12.1 # SAGA (intel)
            Alternatively, you may download and compile Boost libraries yourself: cd ~ && wget https://dl.bintray.com/boostorg/release/1.69.0/source/boost_1_69_0.tar.gz tar -xzvf boost_1_69_0.tar.gz && cd boost_1_69_0 ./bootstrap.sh --with-libraries=program_options,filesystem,system,date_time ./b2 --clean && ./b2 --j12 -a
            Clone and compile MiXeR repository cd ~ && git clone --recurse-submodules -j8 https://github.com/precimed/mixer.git mkdir mixer/src/build && cd mixer/src/build cmake .. && make bgmg -j16 # if you use GCC compiler CC=icc CXX=icpc cmake .. && make bgmg -j16 # if you use Intel compiler cmake .. -DBOOST_ROOT=$HOME/boost_1_69_0 && make bgmg -j16 # if you use locally compiled boost
            The source code is nearly identical, but I've changed the procedure to run MiXeR which is described in this README file. Still, you need to updated the code by git pull. If you updated MiXeR in early summer 2020 there will be no changes in the native C++ code (hense no need to re-compile the libbgmg.so binary), but to be safe it's best to execute cd <MIXER_ROOT>/src/build && cmake .. && make command (after module load relevant modules, as described in this section.)
            If you previously downloaded 1kG reference, you need to download 20 new files called 1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.repNN.snps. Otherwise you need to generate them with mixer.py snps command as described above.
            If you previously generated your input summary statistics constraining them to HapMap3 SNPs, you need to re-generated them without constraining to HapMap3.
            Assuming you have a SLURM script for each MiXeR analysis, you need to turn this script into a job array (#SBATCH --array=1-20) which executes 20 times, and use --extract 1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep${SLURM_ARRAY_TASK_ID}.snps flag in mixer.py fit1 and mixer.py fit2, also adjusting input/output file names accordingly. Example scripts are available in scripts folder.
            To process .json files produced by MiXeR, you now first need to run a mixer_figures.py combine step as shown above. This will combine 20 .json files by averaging individual parameter estimates, and calculating standard errors.
            When you generate figures with mixer_figures.py one and mixer_figures.py two commands and use the "combined" .json files, you'll need to add --statistic mean std to your commands.
            With MiXeR v1.3 you should expect a slightly lower polygenicity estimate, mainly because of --maf 0.05 constraint on the frequency of genetic variants used in the fit procedure. The rationale for --maf 0.05 filter is to still have a robust selection of SNPs in the fit procedure despite not having HapMap3 filter.
            With MiXeR v1.3 you should expect a 10 fold increase in CPU resources needed per ran (20 times more runs, but each run is ~600K SNPs which is half the size of HapMap3).

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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