Package: skewr 1.45.0

Ryan Putney

skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.

Authors:Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]

skewr_1.45.0.tar.gz
skewr_1.45.0.zip(r-4.7)skewr_1.45.0.zip(r-4.6)skewr_1.45.0.zip(r-4.5)
skewr_1.45.0.tgz(r-4.6-any)skewr_1.45.0.tgz(r-4.5-any)
skewr_1.45.0.tar.gz(r-4.7-any)skewr_1.45.0.tar.gz(r-4.6-any)
skewr_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
skewr/json (API)

# Install 'skewr' in R:

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

On BioConductor:skewr-1.45.0(bioc 3.24)skewr-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylation twochannel preprocessing qualitycontrol

3.30 score 4 scripts 6 exports 170 dependencies

Last updated from:4e9359b655. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	440
linux-devel-x86_64	NOTE	670
source / vignettes	OK	637
linux-release-x86_64	NOTE	657
macos-release-arm64	NOTE	325
macos-oldrel-arm64	NOTE	399
windows-devel	NOTE	495
windows-release	NOTE	480
windows-oldrel	NOTE	485
wasm-release	OK	403

Exports:getBarcodes getMethyLumiSet getSNparams panelPlots preprocess subsetProbes

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr evaluate farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread HDF5Array highr hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi mixsmsn multtest mvtnorm nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools ROC Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom wateRmelon withr xfun XML xml2 xtable XVector yaml

An Introduction to the skewr Package

Introduction | Getting Started | Sample Session | Single Plots | sessionInfo

Rendered fromskewr.Rnwusingknitr::knitr

Last update: 2018-08-30
Started: 2015-02-28

Help page	Topics
Get barcodes from idat file names	getBarcodes
Read idat files and create a 'MethyLumiSet' object	getMethyLumiSet
Estimate parameters for finite mixture of Skew-Normal distributions	getSNparams
Plot the distributions of the probe intensities and the components of the skew-normal mixture model	panelPlots
Normalize a MethyLumiSet object using some popular choices	preprocess
Conveniently subset probes by type and retrieve the methylated or unmethylated intensities	subsetProbes

Package: skewr 1.45.0

skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

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