bigstatsr | R package for statistical tools | Data Visualization library

by privefl R Version: Current License: No License

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kandi X-RAY | bigstatsr Summary

bigstatsr is a R library typically used in Analytics, Data Visualization applications. bigstatsr has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

R package {bigstatsr} provides functions for fast statistical analysis of large-scale data encoded as matrices. The package can handle matrices that are too large to fit in memory thanks to memory-mapping to binary files on disk. This is very similar to the format big.matrix provided by R package {bigmemory}, which is no longer used by this package (see the corresponding vignette). As inputs, package {bigstatsr} uses Filebacked Big Matrices (FBM).

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Quality

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Support

bigstatsr has a low active ecosystem.

It has 164 star(s) with 27 fork(s). There are 4 watchers for this library.

It had no major release in the last 6 months.

There are 3 open issues and 127 have been closed. On average issues are closed in 163 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of bigstatsr is current.

Quality

bigstatsr has 0 bugs and 0 code smells.

Security

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

bigstatsr code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bigstatsr does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

bigstatsr releases are not available. You will need to build from source code and install.

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

It has 14181 lines of code, 0 functions and 79 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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bigstatsr Key Features

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bigstatsr Examples and Code Snippets

No Code Snippets are available at this moment for bigstatsr.

Community Discussions

Trending Discussions on bigstatsr

foreach loop in R returns NA values for my array output

How to populate bigstatsr::FBM with sqlite database for later consumption?

QUESTION

foreach loop in R returns NA values for my array output

Asked 2021-Jul-17 at 05:39

I am trying to Apply foreach loop in R for one of my projects since for loop takes very long for output. The problem is foreach loops doesn't update memory and returns NA value. I found that this can be ruled out while creating matrix using the FBM function of bigstatsr package of R, but I have a code that deals with arrays and not 2D matrices. here is the code

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ANSWER

Answered 2021-Jul-17 at 05:39

I guess the part taking time is fitting the models.

So you can always return list(jj, r, ft[,jj,,r]) (or even just ft[,jj,,r]) and fill the array later.

Source https://stackoverflow.com/questions/68385095

QUESTION

How to populate bigstatsr::FBM with sqlite database for later consumption?

Asked 2021-Mar-04 at 06:17

I'm a newbie to the bigstatsr package. I have a sqlite database which I want to convert to an FBM matrix of 40k rows (genes) 60K columns (samples) for later consumption. I found examples of how to populate the matrix with random values but I'm not sure of what would be the best way to populate it with values from my sqlite database.

Currently I do it sequentially, here's some mock code:

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ANSWER

Answered 2021-Mar-04 at 06:17

That is a very good first try that you have by yourself.

What is inefficient here is to test for dplyr::filter(sample == current_sample) for every single sample. I would try to use match() first to get the indices. Then, what would be a bit inefficient is to populate each column individually. As you said, you could use big_apply() to do this by blocks.
big_write() is for writing the FBM to some text file (e.g. csv). What you want here is to use FBM()$save() (second line of the example in the README), and then use big_attach() on the .rds file (next line of the README).

Source https://stackoverflow.com/questions/66465374

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

Vulnerabilities

No vulnerabilities reported

Install bigstatsr

You can download it from GitHub.

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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