ldpred | Python based software package that adjusts GWAS

by bvilhjal Python Version: 1.0.8 License: MIT

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | ldpred Summary

ldpred is a Python library. ldpred has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

LDpred is a Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD). The details of the method is described in Vilhjalmsson et al. (AJHG 2015) [

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ldpred has a low active ecosystem.

It has 75 star(s) with 53 fork(s). There are 11 watchers for this library.

It had no major release in the last 12 months.

There are 35 open issues and 100 have been closed. On average issues are closed in 102 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ldpred is 1.0.8

Quality

ldpred has no bugs reported.

Security

ldpred has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

ldpred is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

ldpred releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions are available. Examples and code snippets are not available.

Top functions reviewed by kandi - BETA

kandi has reviewed ldpred and discovered the below as its top functions. This is intended to give you an instant insight into ldpred implemented functionality, and help decide if they suit your requirements.

Perform Coordinate Coordinates
Verify the coordination data
Filter the coordinate data
Writes coordinate data to HDF5 file
Run LDpred on a given HDFred distance matrix
Calculate the LDAP probability distribution using a posterior distribution
Returns the sample size of the LDAPred distribution
Get constant value
Calculate the risk score for each phenotype
Creates a score file containing only the polygenic effects
Get the phenotypes from a genotype file
Parse the covariates file
Parse pcs file
Convenience wrapper for get_ld_dict
Get the parameter type from a hdf5 file
R Return the status of SNPs in the given position
Shrinks r2 matrix r
Parse the lpred results file
Calculate polygenic risk score
Wrapper function for LDAP - infering
Parse a phenotypes file
Parse summary stats from hdf5 file
Run LDAP fast using LDAP
Write the parameter data in the coordinated file
Parse a PTRES file
Count the number of lines in a file

Get all kandi verified functions for this library.

ldpred Key Features

No Key Features are available at this moment for ldpred.

ldpred Examples and Code Snippets

No Code Snippets are available at this moment for ldpred.

Community Discussions

Trending Discussions on ldpred

If .. else if .. else loop in R

QUESTION

If .. else if .. else loop in R

Asked 2018-Oct-18 at 19:42

I have a rather long loop in R that I am trying to use in order to align two data frames (dosage and ldpred) by the values they have in specific columns. I'll apologise in advance for the wall of text that's going to follow, but it feels like a fairly complex thing (with probably a very simple solution).

The loop is supposed to take the value of string snp from ldpred and find the same string in dosage and then provide the specific row from dosage. Then it is supposed to use the values of two other columns in ldpred and compare them with the corresponding columns in dosage. If the values match then it is supposed to out 1 in a new column. If they match but are in opposite columns, it it supposed to output -1. And that is all fine.

However, the tricky part is that it also is supposed to then switch the values of ldpred to different values and then repeat the same check as above.

If all of that doesn't return 1 or -1 (I.e. the values just don't match for whatever reason) then it is supposed to return 0.

EDIT upon request containing examples of my data and output:

Dosage:

...

ANSWER

Answered 2018-Oct-18 at 15:51

I think in hindsight this was the wrong forum to ask such a specific question which essentially was related to debugging.

For posterity: I have determined the answer to my own question was in fact because the data files were of different sizes. So eventually the genotype variable ended up being a null value and when that was input to the first stage of the if loop it then was outputting a "missing values" error.

Source https://stackoverflow.com/questions/52877322

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

Vulnerabilities

No vulnerabilities reported

Install ldpred

LDpred can be installed using pip on most systems by typing.

Support

I encourage users to extend the code, and adapt it too their needs. Currently there are no formal guidelines set for contributions, and pull requests will be reviewed on a case by case basis.

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