Package: quantro 1.47.0

Stephanie Hicks

quantro: A test for when to use quantile normalization

A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

Authors:Stephanie Hicks [aut, cre], Rafael Irizarry [aut]

quantro_1.47.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
quantro/json (API)

# Install 'quantro' in R:

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

Datasets:

flowSorted - A subset of FlowSorted.DLPFC.450k data set

On BioConductor:quantro-1.47.0(bioc 3.24)quantro-1.46.0(bioc 3.23)

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

normalization preprocessing multiplecomparison microarray sequencing

6.63 score 1 packages 235 scripts 6 mentions 11 exports 147 dependencies

Last updated from:0cd30ba00c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	223
linux-devel-x86_64	NOTE	400
source / vignettes	OK	262
linux-release-x86_64	NOTE	370
macos-release-arm64	NOTE	238
macos-oldrel-arm64	NOTE	218
windows-devel	NOTE	431
windows-release	NOTE	396
windows-oldrel	NOTE	378
wasm-release	OK	220

Exports:anova matboxplot matdensity MSbetween MSwithin quantro quantroPlot quantroPvalPerm quantroStat quantroStatPerm summary

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doParallel doRNG dplyr farver fastmap filelock foreach formatR futile.logger futile.options genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread HDF5Array hms httr httr2 illuminaio IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig 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 S7 scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml

The quantro user's guide

Rendered fromquantro.Rmdusingknitr::rmarkdown

Last update: 2021-06-18
Started: 2019-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Accessors for the 'anova' slot of a quantro object.	anova anova,quantro-method anova.quantro
A subset of FlowSorted.DLPFC.450k data set	flowSorted
Box plots of columns in a matrix	matboxplot
Density plots of columns in a matrix	matdensity
Accessors for the 'MSbetween' slot of a quantro object.	MSbetween MSbetween,quantro-method MSbetween.quantro
Accessors for the 'MSwithin' slot of a quantro object.	MSwithin MSwithin,quantro-method MSwithin.quantro
quantro	quantro-class
Plot results from 'quantro' function.	quantroPlot
Accessors for the 'quantroPvalPerm' slot of a quantro object.	quantroPvalPerm quantroPvalPerm,quantro-method quantroPvalPerm.quantro
Accessors for the 'quantroStat' slot of a quantro object.	quantroStat quantroStat,quantro-method quantroStat.quantro
Accessors for the 'quantroStatPerm' slot of a quantro object.	quantroStatPerm quantroStatPerm,quantro-method quantroStatPerm.quantro
quantro	quantro show
Accessors for the 'summary' slot of a quantro object.	summary summary,quantro-method summary.quantro