mixOmics | Development repository for the Bioconductor package | Genomics library

by mixOmicsTeam R Version: 6.23.2 License: No License

X-Ray Key Features Code Snippets Community Discussions(8)Vulnerabilities Install Support

kandi X-RAY | mixOmics Summary

mixOmics is a R library typically used in Artificial Intelligence, Genomics applications. mixOmics has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This repository contains the R package now hosted on Bioconductor and our stable and development GitHub versions.

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Support

mixOmics has a low active ecosystem.

It has 112 star(s) with 43 fork(s). There are 6 watchers for this library.

It had no major release in the last 12 months.

There are 13 open issues and 184 have been closed. On average issues are closed in 447 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of mixOmics is 6.23.2

Quality

mixOmics has 0 bugs and 0 code smells.

Security

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

mixOmics code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

mixOmics 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

mixOmics releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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mixOmics Key Features

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mixOmics Examples and Code Snippets

No Code Snippets are available at this moment for mixOmics.

Community Discussions

Trending Discussions on mixOmics

Problems installing older version of Bioconductor's mixOmics packages in R

How to use lapply with get.confusion_matrix() in R?

How do I specify a PLS model in tidy models

Predictor importance for PLS model trained with tidymodels

How to perform pslda in R showing error rate for several elements of a list?

How to save plots in list as jpeg using lapply in R?

How to make multiple plots of individual observations with background (splsda model) in R from a list?

How to create new object from columns of dataframe in list in R and use this for modeling in R?

QUESTION

Problems installing older version of Bioconductor's mixOmics packages in R

Asked 2022-Feb-25 at 04:17

I've spent the day trying to load the appropriate package versions in R that I saved in a renv lockfile.

I used the package RVAideMemoire which is tied in with mixOmics in bioconductor, which can't be loaded automatically using renv::restore().

I followed the steps outlined here to install the appropriate version of bioconductor (3.11) to get moxOmics version 6.12.1.

R how to install a specified version of a bioconductor package?

Unfortunately I ended up with mixOmics version 6.14.1. I attempted to load the earlier version using:

...

ANSWER

Answered 2022-Feb-25 at 04:17

BiocManager::install() doesn't provide an interface for installing specific versions of a package. The documentation for the version argument states:

version: 'character(1)' Bioconductor version to install, e.g., 'version = "3.8"'. The special symbol 'version = "devel"' installs the current 'development' version.

That is, it relates to the Bioconductor version, not the package version.

That said, you should be able to use renv to install a specific version of the package from Bioconductor. For example:

Source https://stackoverflow.com/questions/71247393

QUESTION

How to use lapply with get.confusion_matrix() in R?

Asked 2020-Dec-24 at 04:58

I am performing a PLS-DA analysis in R using the mixOmics package. I have one binary Y variable (presence or absence of wetland) and 21 continuous predictor variables (X) with values ranging from 1 to 100. I have made the model with the data_training dataset and want to predict new outcomes with the data_validation dataset. These datasets have exactly the same structure.

My code looks like:

...

ANSWER

Answered 2020-Dec-24 at 04:58

Without reproducible there is no way to test this but you need to convert the code you want to run each time into a function. Something like this:

Source https://stackoverflow.com/questions/65426880

QUESTION

How do I specify a PLS model in tidy models

Asked 2020-Nov-12 at 22:12

I'm interested in learning tidymodels and have tried to apply it to some exercises in Appied Predictive Modeling. This is Exercise 6.2. I would like to specify a Partial Least Squares (PLS) model to the permeability data set.

I have the following code that works all the way up to the tune grid. I've modeled my analysis off of Julia Silge's - Lasso regression with tidymodels and The Office found here.

You can see my script and the tune_grid error message below.

...

ANSWER

Answered 2020-Nov-12 at 22:12

I am guessing that you may be using a Windows computer, because we currently have a bug in the CRAN version of tune for parallel processing on Windows. Try either:

training sequentially without parallel processing, or
installing the development version of tune where we have fixed this bug, via devtools::install_github("tidymodels/tune")

You should see results like this:

Source https://stackoverflow.com/questions/64582463

QUESTION

Predictor importance for PLS model trained with tidymodels

Asked 2020-Oct-19 at 19:20

I'm using tidymodels to fit a PLS model but I'm struggling to find the PLS variable importance scores or coefficients.

This is what I've tried so far; the example data is from AppliedPredictiveModeling package.

Modeling fitting ...

ANSWER

Answered 2020-Oct-19 at 19:20

You can directly tidy() the output of the PLS model to get the coefficients:

Source https://stackoverflow.com/questions/64254295

QUESTION

How to perform pslda in R showing error rate for several elements of a list?

Asked 2020-Aug-07 at 16:49

I am performing a splsda-model in R on 10 dataframes (data of 10 study areas), stored as a list (datalist). All these dataframes are similar, with the same variables, but just different values. I use the micromics library to do this.

This is the head of the first study area. It compares the absence or presence of wetlands (factor variable - wetl or no wetl) depending on its value of TPI of different ranges.

...

ANSWER

Answered 2020-Aug-07 at 16:49

Based on your outputs, you will have to create a new list and save the results on it. Using just myperf_plsda could be overwriting each step in the loop. Also most of the measures you want are lists, so I added some processing functions to reach dataframes. I used next dummy data:

Source https://stackoverflow.com/questions/63301590

QUESTION

How to save plots in list as jpeg using lapply in R?

Asked 2020-Aug-05 at 10:57

I have a list of 10 plots/graphs from model_list for which I used the following code below. I stored these plots in the list var_list.

...

ANSWER

Answered 2020-Aug-05 at 10:57

With data provided in a similar post by you, here a possible solution to your issue. It is better if you work around model_list because when you transform to var_list all data become graphical elements. Next code contains a replicate of model_list using datalist but in your real problem you must have it, also must include names for each of the components of the list:

Source https://stackoverflow.com/questions/63231376

QUESTION

How to make multiple plots of individual observations with background (splsda model) in R from a list?

Asked 2020-Aug-04 at 16:38

I am performing a splsda-model in R on 10 dataframes (data of 10 study areas), stored as a list (datalist). All these dataframes are similar, with the same variables, but just different values.

...

ANSWER

Answered 2020-Aug-04 at 16:38

With the sample data you provided, here a solution to save in one pdf each of the plots. For the sake of making reproducible the exercise, I have created datalist with the input you added. In your real problem you must have datalist with names in order to add the titles to plots. Also some data for plots was not available like datastudyarea1 but it will not be difficult completing that part of the code for you. Here is the sketch:

Source https://stackoverflow.com/questions/63249470

QUESTION

How to create new object from columns of dataframe in list in R and use this for modeling in R?

Asked 2020-Jul-30 at 13:13

I have a list of 10 dataframes, called "datalist", on which I want to apply several functions. I am quite new to R. I searched on the internet but can't find the right solution.

The dataframes all have the same variables, like simplified example below:

...

ANSWER

Answered 2020-Jul-30 at 13:13

You can write a custom model fitting function to subset the data.frames selecting just the columns of interest and run the modeling function.
lapply the custom function to the data list and select the loadings from this output list with a *apply loop.

Source https://stackoverflow.com/questions/63172622

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

Vulnerabilities

No vulnerabilities reported

Install mixOmics

(Mac OS Users Only:) Ensure you have installed XQuartz first. Make sure you have the latest R version and the latest BiocManager package installed following these instructions (if you use legacy R versions (<=3.5.0) refer to the instructions at the end of the mentioned page).

Support

We welcome community contributions concordant with our code of conduct. We strongly recommend adhering to Bioconductor’s coding guide for software consistency if you wish to contribute to mixOmics R codes.

Find more information at: