Package: doppelgangR 1.41.0

Levi Waldron

doppelgangR: Identify likely duplicate samples from genomic or meta-data

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

Authors:Levi Waldron [aut, cre], Markus Reister [aut, ctb], Marcel Ramos [ctb]

doppelgangR_1.41.0.tar.gz
doppelgangR_1.41.0.zip(r-4.7)doppelgangR_1.41.0.zip(r-4.6)doppelgangR_1.41.0.zip(r-4.5)
doppelgangR_1.41.0.tgz(r-4.6-any)doppelgangR_1.41.0.tgz(r-4.5-any)
doppelgangR_1.41.0.tar.gz(r-4.7-any)doppelgangR_1.41.0.tar.gz(r-4.6-any)
doppelgangR_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
doppelgangR/json (API)

# Install 'doppelgangR' in R:

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

Bug tracker:https://github.com/lwaldron/doppelgangr/issues

Pkgdown/docs site:https://waldronlab.github.io

On BioConductor:doppelgangR-1.41.0(bioc 3.24)doppelgangR-1.40.0(bioc 3.23)

immunooncology rnaseq microarray geneexpression qualitycontrol bioconductor-package

7.13 score 5 stars 36 scripts 374 downloads 3 mentions 19 exports 68 dependencies

Last updated from:94a7be768e. Checks:1 WARNING, 5 NOTE, 2 OK, 2 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	193
linux-devel-x86_64	NOTE	374
source / vignettes	OK	320
linux-release-x86_64	NOTE	392
macos-release-arm64	NOTE	379
macos-oldrel-arm64	ERROR	163
windows-devel	NOTE	648
windows-release	NOTE	705
windows-oldrel	ERROR	561
wasm-release	OK	171

Exports:colFinder corFinder doppelgangR dst mst.mle outlierFinder phenoDist phenoFinder plot print pst qst rst show smokingGunFinder st.mle summary vectorHammingDist vectorWeightedDist

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI DelayedArray digest edgeR fastmap formatR futile.logger futile.options genefilter generics GenomicRanges glue httr impute IRanges jsonlite KEGGREST lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats memoise mgcv mime mnormt nlme openssl pkgconfig png R6 rlang RSQLite S4Arrays S4Vectors Seqinfo snow SparseArray statmod SummarizedExperiment survival sva sys vctrs XML xtable XVector

doppelgängR

Rendered fromdoppelgangR.Rmdusingknitr::rmarkdown

Last update: 2025-11-17
Started: 2016-03-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Identify likely duplicate samples from genomic or meta-data	doppelgangR-package
Calculate pairwise similarities of colData between samples for a list containing two DataFrame	colFinder
Calculate pair-wise correlations between samples using the expr() slots of a list of two ExpressionSets.	corFinder
DoppelGang S4 class	DoppelGang DoppelGang-class print,DoppelGang-method show,DoppelGang-method summary,DoppelGang-method
doppelgangR	doppelgangR
Skew-t Distribution	dst pst qst rst
Maximum likelihood estimation for a (multivariate) skew-t distribution	mst.mle st.mle
Identifies outliers in a similarity matrix.	outlierFinder
Calculate distance between two vectors, rows of one matrix/dataframe, or rows of two matrices/dataframes.	phenoDist
Calculate pairwise similarities of phenoData between samples for a list containing two ExpressionSets	phenoFinder
Histograms of all pairwise sample correlations, showing identified doppelgangers.	plot,DoppelGang plot,DoppelGang,ANY-method plot,DoppelGang-method plot-methods plot.DoppelGang plot.doppelgangR
Find doppelgangers based on "smoking gun" phenotypes - those that should be unique to each patient.	smokingGunFinder
Calculate Hamming Distance between two vectors, using pairwise complete observations.	vectorHammingDist
Calculate a weighted distance between two vectors, using pairwise complete observations.	vectorWeightedDist