Package: skewr 1.37.0

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]

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skewr.pdf |skewr.html✨
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-1.37.0(bioc 3.20)skewr-1.36.0(bioc 3.19)

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

bioconductor-package

6 exports 0.91 score 161 dependencies

Last updated 2 months agofrom:af6e1a649f

Exports:getBarcodes getMethyLumiSet getSNparams panelPlots preprocess subsetProbes

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr evaluate fansi farver fastmap FDb.InfiniumMethylation.hg19 foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable HDF5Array highr hms httr 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 munsell mvtnorm nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools ROC Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales scrime 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 zlibbioc

An Introduction to the skewr Package

Rendered fromskewr.Rnwusingknitr::knitron Jul 01 2024.

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 1.37.0

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

An Introduction to the skewr Package

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Usage by other packages (reverse dependencies)