IntrinsicScan
This is the development version of IntrinsicScan; to use it, please install the devel version of Bioconductor.
Label-Blind Feature-Wise Intrinsic Binary Partition Scanning
Bioconductor version: Development (3.24)
Scans continuous molecular features for intrinsic binary partitions without using phenotype labels to determine the split. For each feature, observations are divided into two one-dimensional states by selecting the split that minimizes the total within-state L1 loss, defined here as the sum of absolute distances between each observation and the medoid of its assigned state. Thus, unlike a squared-error objective, deviations are measured according to their absolute magnitude rather than being squared. Binary phenotype labels are used only after the partition is fixed to orient the two states, quantify phenotype concordance using orientation-free Youden J, perform exact conditional inference, and optionally assess resampling stability or fixed-partition permutation calibration. The method is intended for preprocessed continuous omics measurements and does not imply that a fitted partition represents true biological bimodality or discrete biological states.
Author: Leandro Altare [aut, cre]
Maintainer: Leandro Altare <memedesimo22 at gmail.com>
citation("IntrinsicScan")):
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("IntrinsicScan")
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("IntrinsicScan")| IntrinsicScan: label-blind feature-wise binary partitioning | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, GeneExpression, Microarray, RNASeq, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | Biobase, S4Vectors, SummarizedExperiment, withr |
| System Requirements | |
| URL | https://github.com/memedesimo98/IntrinsicScan |
| Bug Reports | https://github.com/memedesimo98/IntrinsicScan/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, leukemiasEset, 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 | IntrinsicScan_0.99.4.tar.gz |
| Windows Binary (x86_64) | IntrinsicScan_0.99.4.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | IntrinsicScan_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | IntrinsicScan_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/IntrinsicScan |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/IntrinsicScan |
| Bioc Package Browser | https://code.bioconductor.org/browse/IntrinsicScan/ |
| Package Short Url | https://bioconductor.org/packages/IntrinsicScan/ |
| Package Downloads Report | Download Stats |