UTMOST | unified test for molecular signatures | Genomics library
kandi X-RAY | UTMOST Summary
kandi X-RAY | UTMOST Summary
UTMOST (Unified Test for MOlecular SignaTures) is a principled method to perform cross-tissue expression imputation and gene-level association analysis. The preprint could be found at A statistical framework for cross-tissue transcriptome-wide association analysis.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Initializes preprocess column UI
- Processes a results file .
- Load a matrix from a file .
- Build the work object .
- Load covariance matrix .
- Reads a gipped source file .
- build IMPUTE utils
- Calculate normalized normalization from reference data .
- Load data from digest file .
- Get SNPs from a given gene matrix .
UTMOST Key Features
UTMOST Examples and Code Snippets
Community Discussions
Trending Discussions on UTMOST
QUESTION
Here goes. I have a 200-line MySQL query that contains six different Excel formulas in one of the columns, like this:
...ANSWER
Answered 2022-Mar-31 at 16:09HEREDOC does the trick. The following code does not get mangled:
QUESTION
*** EDIT - I know it is a long post and I know I have used some 'interesting' language choices. And, I'm choosing to believe the three answers I've had so far were made with good intent - for that I thank you. But, I really must insist, if you are not willing to read the whole post thoroughly or if you don't understand what it is I am actually asking, please save both our time and refrain from posting. ***
I have been searching for an answer to exactly the same question posed here - same online course, same lecturer; I recognise the code from the video.
I quickly found solutions in the form of #define and using an enum, but that still didn't really solve how the lecturer got his code to compile; and, I would like to actually comprehend, not just make it work so, I tried to dig deeper.
The professor in question doesn't ever actually show the code compilation, it's always a "here's one I compiled earlier" scenario - so I had included the possibility the error was in that unseen stage as indicated by the two answers on the page: he may well have been using g++ or clang.
However, my search was most circuitous, leading me hither and tither across the net, and in my quest, before I came across the above linked answers and amongst other things I came across this video where at around the 9 minute mark he compiles this code:
...ANSWER
Answered 2022-Jan-03 at 23:29This is a result of constant folding in the clang compiler.
The instructor is compiling the program on a Mac, and on that platform "gcc" is an alias for "clang". While gcc does not perform this folding for a VLA, clang does.
From the clang documentation (version 10):
Differences between all c* and gnu* modes:
- c* modes define
__STRICT_ANSI__.- Target-specific defines not prefixed by underscores, like “linux”, are defined in gnu* modes.
- Trigraphs default to being off in gnu* modes; they can be enabled by the -trigraphs option.
- The parser recognizes
asmandtypeofas keywords in gnu* modes; the variants__asm__and__typeof__are recognized in all modes.- The Apple “blocks” extension is recognized by default in gnu* modes on some platforms; it can be enabled in any mode with the
-fblocksoption.- Arrays that are VLA’s according to the standard, but which can be constant folded by the frontend are treated as fixed size arrays. This occurs for things like
int X[(1, 2)];, which is technically a VLA. c * modes are strictly compliant and treat these as VLAs.
QUESTION
I have text in below format. I need to extract PolicyNumber and Code from these
...ANSWER
Answered 2021-Dec-02 at 13:00You could use stringr with look behind notation.
QUESTION
I just wanted to know if there is a way to delete or modify a table from flask-sqlalchemy.
I am working on a flask web app for my final project (second time using flask). I just (1 month ago) switched to flask sqlalchemy as my project is on Heroku I had to connect my table to Heroku PostgreSQL. I made a flask-sqlalchemy table and created it using the db.create_all() command now for my app to fulfil its purpose it is of utmost importance to save images, the best way of which I found to be to add them to the database. Now I want to change the particular table class to store a column called image as image = db.Column(db.Text, nullable=False) but I can not. It remains the former and gives me an error signifying that the column image does not exist every time I try to access or add something to the table. Any intention or will to help is appreciated.
ANSWER
Answered 2021-Nov-19 at 09:01You can use drop()
QUESTION
good afternoon! hi all! 1st time posting
for my assignment we are filling arrays using arithmetic and nested for loops. i've done a complete filling of a 2D array before using prime numbers, although i think i'm messing up somewhere..
when doing the line int priorNum = arr[r-1][c]; (see full code below) i run into an exception. i am trying to overwrite other lines in my array with this new equation, but must i be stopped by this utmost unchivalrous java error.
the error: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 10
my array: int[][] arrayDimension = new int[10][6];
ANSWER
Answered 2021-Nov-11 at 08:59The problem I can see is that in the first iteration when int priorNum = arr[r-1][c]; gets executed, r = 0, as specified by your outer for loop.
So you are basically trying to access an element of your 2D array using a negative index, which will result in an ArrayIndexOutOfBoundException being thrown.
You could adopt an if statement that will handle the first iteration so that you will not access a prior index.
You could also look at the Array access section of the following article: https://docs.oracle.com/javase/specs/jls/se7/html/jls-10.html
Hope this helped.
QUESTION
I was just trying to make a dropdown menu. But what my dropdown menu is doing that it is making the slide below it more go down. I have also attached the HTML and the CSS file. So that you can have a look. If you will run the code, it would not run properly as there is no image attached. Just assume that there is a slider below the dropdown buttons consisting of 5 images change in every 3 seconds. Actually it takes the slider go more down as to show all the content but still after opening the full dropdown it just show 1 link inside of it. So baically there are two errors one it is taking the slider down and second it does not show all the content. I am a beginner at coding, so there could be possible that I have done some silly errors in the code. So just requesting you to pls help me.
...ANSWER
Answered 2021-Oct-22 at 18:11If you make the nav position:absolute, then position with left, top etc, this will stop it from affecting other element as it expands.
QUESTION
When looping through a NativeArray of float4[], and wanting to set one of the 'fields' of each float4 (let's say y) to a value, it doesn't seem immediately possible because it's a temporary value.
this:
...ANSWER
Answered 2021-Sep-28 at 13:19As usual for any struct (= value) type if it is within an array you can only do
QUESTION
I have an outer foreach/dopar parallel loop containing an inner loop. Every instance of the inner loop should work on the same set of random numbers. The rest, i.e. the remaining parts of the outer body and the parallel instances should work as usual, i.e. with independent random numbers.
I can achieve this in a non-parallel implementation by saving the state of the RNG before the start of the inner loop and restoring this state after execution of each instance of the inner loop. See the following example:
...ANSWER
Answered 2021-Sep-21 at 12:08You could try using set.seed(seed=NULL) to reset the seed, which is essentially the same as selecting a random seed, I think.
QUESTION
no_of_stars = int(input("Please enter number of rows you want to print\n"))
def print_positive():
while no_of_stars >0:
print(no_of_stars*("*"), end= '\n')
no_of_stars -=1
print_positive()
ANSWER
Answered 2021-Jun-30 at 11:18Anyone receiving the same problem leave all the local variable scope etc. things aside and just put
QUESTION
I'm currently working through my first implementation of a Jekyll webpage (via Github-pages) and I'm trying to use the Poole: Lanyon structure. However, while it seems that the static site is active, it is not picking up any of the formatting.
I can't tell if I needed to add anything else from lanyon github page (https://github.com/poole/lanyon) or if it could have something to do with my '_config' file, which currently looks as follows (or is an entirely different issue):
...ANSWER
Answered 2021-Jun-24 at 02:56Looks like I was overthinking this issue - the following was my simple solution:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install UTMOST
--model_db_path Path to gene expression imputation model (estimated weights/effect sizes of cis-eQTLs).
--covariance Path to file containing covariance information (used to estimate the variance of gene-level effect size estimator, see Gene-level association test in Methods section of manuscript for details).
--gwas_folder Folder containing GWAS summary statistics data.
--gwas_file_pattern The file patten of gwas file (file name of summary statistics if not segmented by chromosomes).
--snp_column Argument with the name of the column containing the RSIDs.
--effect_allele_column Argument with the name of the column containing the effect allele.
--non_effect_allele_column Argument with the name of the column containing the non-effect allele.
--beta_column The column containing -effect size estimator for each SNP- in the input GWAS files.
--pvalue_column The column containing -PValue for each SNP- in the input GWAS files.
--output_file Path where results will be saved to.
--verbosity Log verbosity level. 1 means everything will be logged. 10 means high level messages will be logged.
--weight_db Name of weight db in data folder (imputation models).
--input_folder Name of folder containing single-tissue association results (generated in Section 4.1).
--cov_dir Path where covariance results are (covariance matrix for gene-level test statistics across tissues, see Gene-level association test in Methods section of manuscript for details).
--output_dir Path where results will be saved to.
--gene_info File containing the all the genes tested.
--start_gene_index Index of the starting gene in intermediate/gene_info.txt (for parallel computing purpose, could test multiple gene at the same time to reduce computation time).
--end_gene_index Index of the ending gene in intermediate/gene_info.txt (for parallel computing purpose, could test multiple gene at the same time to reduce computation time).
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
