Package: rCGH 1.43.0

Frederic Commo

rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Authors:Frederic Commo [aut, cre]

rCGH_1.43.0.tar.gz
rCGH_1.43.0.zip(r-4.7)rCGH_1.43.0.zip(r-4.6)rCGH_1.43.0.zip(r-4.5)
rCGH_1.43.0.tgz(r-4.6-any)rCGH_1.43.0.tgz(r-4.5-any)
rCGH_1.43.0.tar.gz(r-4.7-any)rCGH_1.43.0.tar.gz(r-4.6-any)
rCGH_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rCGH/json (API)

# Install 'rCGH' in R:

install.packages('rCGH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fredcommo/rcgh/issues

Datasets:

agilentDB - ACGH Agilent Probes GC Fraction
hg18 - Hg18 Chromosome Lengths and Centromere Locations
hg19 - Hg19 Chromosome Lengths and Centromere Locations
hg38 - Hg38 Chromosome Lengths and Centromere Locations

On BioConductor:rCGH-1.43.0(bioc 3.24)rCGH-1.42.0(bioc 3.23)

acgh copynumbervariation preprocessing featureextraction

5.47 score 5 stars 1 packages 33 scripts 540 downloads 2 mentions 20 exports 114 dependencies

Last updated from:834c831ded. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	324
linux-devel-x86_64	NOTE	658
source / vignettes	OK	513
linux-release-x86_64	NOTE	633
macos-release-arm64	NOTE	362
macos-oldrel-arm64	NOTE	295
windows-devel	NOTE	510
windows-release	NOTE	535
windows-oldrel	NOTE	524
wasm-release	OK	288

Exports:adjustSignal byGeneTable EMnormalize getCNset getInfo getParam getSegTable multiplot plotDensity plotLOH plotProfile readAffyCytoScan readAffyOncoScan readAffySNP6 readAgilent readGeneric recenter<-segmentCGH setInfo<-view

Dependencies:abind aCGH affy affyio AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bslib cachem cigarillo cli cluster codetools commonmark cpp11 crayon curl DBI DelayedArray digest DNAcopy farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable htmltools httpuv httr IRanges isoband jquerylib jsonlite KEGGREST labeling lambda.r later lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime multtest openssl org.Hs.eg.db otel pkgconfig plyr png preprocessCore promises R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shiny snow sourcetools SparseArray statmod SummarizedExperiment survival sys TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene vctrs viridisLite withr XML xtable XVector yaml

using rCGH package

Rendered fromrCGH.Rnwusingknitr::knitr

Last update: 2017-11-30
Started: 2015-07-09

Help page	Topics
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data	rCGH-package rCGH
Array-based CGH Preprocessing	adjustSignal adjustSignal,rCGH-method adjustSignal-methods
aCGH Agilent Probes GC Fraction	agilentDB
'"rCGH"' Accessor Functions	Accessors AllAccessors getCNset getCNset,rCGH-method getCNset-methods getInfo getInfo,rCGH-method getInfo-methods getParam getParam,rCGH-method getParam-methods getSegTable getSegTable,rCGH-method getSegTable-methods
Converting a Segmentation Table Into a By-Gene Table	byGeneTable
Genomic Profile Centralization	EMnormalize EMnormalize,rCGH-method EMnormalize-methods
Hg18 Chromosome Lengths and Centromere Locations	hg18
Hg19 Chromosome Lengths and Centromere Locations	hg19
Hg38 Chromosome Lengths and Centromere Locations	hg38
Static Genomic Profile and LOH Visualization	multiplot multiplot,rCGH-method multiplot-methods
Visualizing the Log2Ratios Density and Centralization Decision	plotDensity plotDensity,rCGH-method plotDensity-methods
Allelic Differences Visualization	plotLOH plotLOH,rCGH-method plotLOH-methods
Static Genomic Profile Visualization	plotProfile plotProfile,rCGH-method plotProfile-methods
Class '"rCGH-Agilent"'	rCGH-Agilent-class
Class '"rCGH"'	rCGH-class
Class '"rCGH-cytoScan"'	rCGH-cytoScan-class
Class '"rCGH-generic"'	rCGH-generic-class
Class '"rCGH-oncoScan"'	rCGH-oncoScan-class
Class '"rCGH-SNP6"'	rCGH-SNP6-class
Affymetrix CytoScanHD '"rCGH-cytoScan"' Constructor	readAffyCytoScan
Affymetrix OncoScan '"rCGH-oncoScan"' Constructor	readAffyOncoScan
Affymetrix SNP6 '"rCGH-SNP6"' Constructor	readAffySNP6
Agilent Dual-Color Hybridization '"rCGH-Agilent"' Constructor.	readAgilent
Generic rCGH object '"rCGH-generic"' Constructor	readGeneric
Recentering a Genomic Profile	recenter recenter<- recenter<-,rCGH-method recenter<--methods
Genomic Profile Segmentation	segmentCGH segmentCGH,rCGH-method segmentCGH-methods
Adding Information In An Object Of Class '"rCGH"'	setInfo setInfo<- setInfo<-,rCGH-method setInfo<--methods
'show' '"rCGH"'	show,rCGH-method show-methods
Interactive Genomic Profile Visualization	view view,rCGH-method view-methods

Package: rCGH 1.43.0

rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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