tilingArray
This is the released version of tilingArray; for the devel version, see tilingArray.
Transcript mapping with high-density oligonucleotide tiling arrays
Bioconductor version: Release (3.23)
The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.
Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Maintainer: Zhenyu Xu <zxu at embl.de>
citation("tilingArray")):
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("tilingArray")
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("tilingArray")| Introduction to the plotAlongChrom function | R Script | |
| Introduction to using the segment function to fit a piecewise constant curve | R Script | |
| Normalisation with the normalizeByReference function in the tilingArray package | ||
| Segmentation demo | ||
| Supplement. Calculation of the cost matrix | ||
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, Software, Visualization |
| Version | 1.90.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.11.0), Biobase, methods, pixmap |
| Imports | strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | davidTiling |
| Imports Me | ADaCGH2 |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tilingArray_1.90.0.tar.gz |
| Windows Binary (x86_64) | tilingArray_1.90.0.zip |
| macOS Binary (big-sur-x86_64) | tilingArray_1.90.0.tgz |
| macOS Binary (sonoma-arm64) | tilingArray_1.90.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tilingArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tilingArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/tilingArray/ |
| Package Short Url | https://bioconductor.org/packages/tilingArray/ |
| Package Downloads Report | Download Stats |