wavFeatExt
This is the released version of wavFeatExt; for the devel version, see wavFeatExt.
Wavelet-based Feature Extraction for Copy-number Alteration Data
Bioconductor version: Release (3.23)
Provides tools for simulating copy-number alteration (CNA) profiles, applying a non-decimated Haar wavelet transform to genomic signals, and extracting wavelet-derived features for use in supervised learning. Multiple machine learning methods including lasso and elastic-net regularisation, random forest, partial least squares, neural networks and k-nearest neighbours are implemented to train predictive models from genomic feature vectors. The workflow enables end-to-end analysis from CNA simulation to feature extraction and classification.
Author: Maharani Ahsani Ummi [aut, cre], Arief Gusnanto [aut]
Maintainer: Maharani Ahsani Ummi <maharaniahsani at itb.ac.id>
citation("wavFeatExt")):Maharani Ahsani Ummi, Arief Gusnanto. wavFeatExt: Wavelet-based Feature Extraction for Copy-number Alteration Data. doi:10.18129/B9.bioc.wavFeatExt, R package version 1.0.0, https://bioconductor.org/packages/wavFeatExt.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("wavFeatExt")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("wavFeatExt")| Introduction to wavFeatExt | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, CopyNumberVariation, FeatureExtraction, GenomicVariation, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.5) |
| Imports | DNAcopy, wavethresh, MASS, randomForest, glmnet, pROC, neuralnet, e1071, class, caret, ica, stats, graphics, utils, pls, matrixStats |
| System Requirements | |
| URL | https://github.com/maharaniau/wavFeatExt |
| Bug Reports | https://github.com/maharaniau/wavFeatExt/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | wavFeatExt_1.0.0.tar.gz |
| Windows Binary (x86_64) | wavFeatExt_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | wavFeatExt_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | wavFeatExt_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/wavFeatExt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/wavFeatExt |
| Package Short Url | https://bioconductor.org/packages/wavFeatExt/ |
| Package Downloads Report | Download Stats |