Package: funtooNorm 1.31.0

Kathleen Klein

funtooNorm: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

Authors:Celia Greenwood <[email protected]>,Stepan Grinek <[email protected]>, Maxime Turgeon <[email protected]>, Kathleen Klein <[email protected]>

funtooNorm_1.31.0.tar.gz
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funtooNorm.pdf |funtooNorm.html✨
funtooNorm/json (API)
NEWS

# Install 'funtooNorm' in R:

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

On BioConductor:funtooNorm-1.31.0(bioc 3.21)funtooNorm-1.30.0(bioc 3.20)

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

dnamethylation preprocessing normalization

3.70 score 204 downloads 5 mentions 11 exports 138 dependencies

Last updated 3 months agofrom:4e274a7066. Checks:1 OK, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Dec 29 2024
R-4.5-win	WARNING	Dec 31 2024
R-4.5-linux	WARNING	Dec 29 2024
R-4.4-win	WARNING	Dec 31 2024
R-4.4-mac	WARNING	Dec 29 2024
R-4.3-win	WARNING	Nov 29 2024
R-4.3-mac	WARNING	Dec 29 2024

Exports:agreement fromGenStudFiles fromRGChannelSet funtooNorm getGRanges getNormBeta getNormM getRawBeta getSnpM plotValidationGraph show

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi fastmap foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue HDF5Array hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest illuminaio IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig plogr pls plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 xtable XVector yaml zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
funtooNorm	funtooNorm-package
Function to measure intra-replicate agreement for methylation data.	agreement
Creates a S4 object of class 'SampleSet' from GenomeStudio files	fromGenStudFiles
Creates an object of class SampleSet from a RGChannelSet minfi	fromRGChannelSet
The funtooNorm normalization function	funtooNorm funtooNorm,SampleSet-method
Build GRange object of methylation probes	getGRanges getGRanges,SampleSet-method
Computes Beta values from normalized signals	getNormBeta getNormBeta,SampleSet-method
Computes M values,log2(Meth/Unmeth), from normalized signals	getNormM getNormM,SampleSet-method
Computes Beta value from raw signals	getRawBeta getRawBeta,SampleSet-method
Computes M values after normalization of SNP data.	getSnpM getSnpM,SampleSet-method
plot of Validation Graph for determing number of components	plotValidationGraph plotValidationGraph,SampleSet-method
S4 class object SampleSet	SampleSet-class
Show Object SampleSet	show,SampleSet-method

Usage by other packages (reverse dependencies)