Package: quantro 1.39.0

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]

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quantro.pdf |quantro.html✨
quantro/json (API)
NEWS

# 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-1.39.0(bioc 3.20)quantro-1.38.0(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

11 exports 1.38 score 141 dependencies 2 dependents 6 mentions

Last updated 2 months agofrom:f8b5d9d0d4

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

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doParallel doRNG dplyr fansi farver fastmap foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable HDF5Array hms httr illuminaio IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime minfi multtest munsell nlme nor1mix openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales scrime siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

The quantro user's guide

Stephanie C. Hicks, Rafael Irizarry

Rendered fromquantro.Rmdusingknitr::rmarkdownon Jun 30 2024.

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