Package: COCOA 2.27.0

John Lawson

COCOA: Coordinate Covariation Analysis

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.

Authors:John Lawson [aut, cre], Nathan Sheffield [aut], Jason Smith [ctb]

COCOA_2.27.0.tar.gz
COCOA_2.27.0.zip(r-4.7)COCOA_2.27.0.zip(r-4.6)COCOA_2.27.0.zip(r-4.5)
COCOA_2.27.0.tgz(r-4.6-any)COCOA_2.27.0.tgz(r-4.5-any)
COCOA_2.27.0.tar.gz(r-4.7-any)COCOA_2.27.0.tar.gz(r-4.6-any)
COCOA_2.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
COCOA/json (API)

# Install 'COCOA' in R:

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

Bug tracker:https://github.com/databio/cocoa/issues

Pkgdown/docs site:https://code.databio.org

Datasets:

atf3_chr1 - Atf3 binding regions.
brcaATACCoord1 - A GRanges object with coordinates for select BRCA ATAC-seq peak regions from chr1.
brcaATACData1 - A matrix with ATAC-seq counts in select peak regions from chromosome 1 for 37 patients.
brcaMCoord1 - A GRanges object with genomic coordinates for cytosines from chr1 for the package's built-in DNA methylation data
brcaMetadata - A data.frame with patient metadata for breast cancer patients.
brcaMethylData1 - A matrix with DNA methylation levels from some CpGs on chromosome 1
brcaPCScores - A matrix with principal component scores for PCs 1-4 for four breast cancer patients.
brcaPCScores657 - A data.frame with principal component scores for PCs 1-4 for 657 breast cancer patients as well as a column with estrogen receptor status.
esr1_chr1 - Estrogen receptor alpha binding regions.
gata3_chr1 - Gata3 binding regions.
nrf1_chr1 - Nrf1 binding regions.
rsScores - Example COCOA Results

On BioConductor:COCOA-2.27.0(bioc 3.24)COCOA-2.26.0(bioc 3.23)

epigenetics dnamethylation atacseq dnaseseq methylseq methylationarray principalcomponent genomicvariation generegulation genomeannotation systemsbiology functionalgenomics chipseq sequencing immunooncology dna-methylation pca

7.33 score 11 stars 26 scripts 13 mentions 14 exports 117 dependencies

Last updated from:b65d393262. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	244
linux-devel-x86_64	NOTE	494
source / vignettes	OK	433
linux-release-x86_64	NOTE	483
macos-release-arm64	NOTE	265
macos-oldrel-arm64	NOTE	221
windows-devel	NOTE	378
windows-release	NOTE	351
windows-oldrel	NOTE	397
wasm-release	OK	204

Exports:aggregateSignal aggregateSignalGRList convertToFromNullDist getGammaPVal getMetaRegionProfile getPermStat getTopRegions plotAnnoScoreDist regionQuantileByTargetVar rsRankingIndex rsScoreHeatmap runCOCOA runCOCOAPerm signalAlongAxis

Dependencies:abind askpass assorthead beachmat BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops BSgenome bsseq cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DelayedArray DelayedMatrixStats digest dir.expiry doParallel dplyr farver filelock fitdistrplus foreach formatR futile.logger futile.options generics GenomicAlignments GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable gtools h5mread HDF5Array httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mime MIRA openssl permute pillar pkgconfig png purrr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo shape simpleCache snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XML XVector yaml

Introduction to Coordinate Covariation Analysis

Rendered fromIntroToCOCOA.Rmdusingknitr::rmarkdown

Last update: 2020-10-10
Started: 2018-10-25

Help page	Topics
Score a region set using feature contribution scores	aggregateSignal
Score many region sets	aggregateSignalGRList
Atf3 binding regions.	atf3_chr1
A GRanges object with coordinates for select BRCA ATAC-seq peak regions from chr1.	brcaATACCoord1
A matrix with ATAC-seq counts in select peak regions from chromosome 1 for 37 patients.	brcaATACData1
A GRanges object with genomic coordinates for cytosines from chr1 for the package's built-in DNA methylation data	brcaMCoord1
A data.frame with patient metadata for breast cancer patients.	brcaMetadata
A matrix with DNA methylation levels from some CpGs on chromosome 1	brcaMethylData1
A matrix with principal component scores for PCs 1-4 for four breast cancer patients.	brcaPCScores
A data.frame with principal component scores for PCs 1-4 for 657 breast cancer patients as well as a column with estrogen receptor status.	brcaPCScores657
Coordinate Covariation Analysis (COCOA)	COCOA
Converts COCOA permutation results to null distributions and vice versa	convertToFromNullDist
Estrogen receptor alpha binding regions.	esr1_chr1
Gata3 binding regions.	gata3_chr1
Get a p-value for region set scores based on a gamma distribution.	getGammaPVal
Create a "meta-region" profile	getMetaRegionProfile
Get p-value or z-score based on permutation results	getPermStat
Get regions that are most associated with target variable	getTopRegions
Nrf1 binding regions.	nrf1_chr1
Plot ranked region set scores, annotating groups of interest	plotAnnoScoreDist
Visualize how individual regions are associated with target variable	regionQuantileByTargetVar
Get indices for top scored region sets	rsRankingIndex
Heatmap of region set scores	rsScoreHeatmap
Example COCOA Results (made up)	rsScores
Run COCOA: quantify inter-sample variation, score region sets	runCOCOA
Run COCOA permutations to get p-values	runCOCOAPerm
Visualize how genomic signal in a region set changes along a given axis	signalAlongAxis

Package: COCOA 2.27.0

COCOA: Coordinate Covariation Analysis

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)