Lheuristic
This is the development version of Lheuristic; for the stable release version, see Lheuristic.
Detection of scatterplots with L-shaped pattern
Bioconductor version: Development (3.24)
The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.
Author: Sanchez Pla Alex [aut, cre]
, Miro Cau Berta [aut]
Maintainer: Sanchez Pla Alex <asanchez at ub.edu>
citation("Lheuristic")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Lheuristic")
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("Lheuristic")| L-shaped selection from methylation and expression | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, MethylationArray, Software, StatisticalMethod |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | Hmisc, stats, energy, grDevices, graphics, utils, MultiAssayExperiment, ggplot2, ggpubr |
| System Requirements | |
| URL | https://github.com/ASPresearch/Lheuristic |
| Bug Reports | https://github.com/ASPresearch/Lheuristic/issues |
See More
| Suggests | 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 | Lheuristic_1.5.0.tar.gz |
| Windows Binary (x86_64) | Lheuristic_1.5.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Lheuristic_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | Lheuristic_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Lheuristic |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Lheuristic |
| Bioc Package Browser | https://code.bioconductor.org/browse/Lheuristic/ |
| Package Short Url | https://bioconductor.org/packages/Lheuristic/ |
| Package Downloads Report | Download Stats |