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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 (>= 4.6) |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/wavFeatExt/ |
| Package Short Url | https://bioconductor.org/packages/wavFeatExt/ |
| Package Downloads Report | Download Stats |