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).

Author
Levi Waldron, Markus Riester, Marcel Ramos
Date of publication
None
Maintainer
Levi Waldron <lwaldron.research@gmail.com>
License
GPL (>=2.0)
Version
1.2.0
URLs

View on Bioconductor

Man pages

corFinder
Calculate pair-wise correlations between samples using the...
DoppelGang-class
DoppelGang S4 class
doppelgangR
doppelgangR
doppelgangR-package
Identify likely duplicate samples from genomic or meta-data
dst
Skew-t Distribution
mst.mle
Maximum likelihood estimation for a (multivariate) skew-t...
outlierFinder
Identifies outliers in a similarity matrix.
phenoDist
Calculate distance between two vectors, rows of one...
phenoFinder
Calculate pairwise similarities of phenoData between samples...
plot-methods
Histograms of all pairwise sample correlations, showing...
print-methods
Print a DoppelGang object
show-methods
Show a DoppelGang object
smokingGunFinder
Find doppelgangers based on "smoking gun" phenotypes - those...
summary-methods
Summarizes a DoppelGang object
vectorHammingDist
Calculate Hamming Distance between two vectors, using...
vectorWeightedDist
Calculate a weighted distance between two vectors, using...

Files in this package

doppelgangR/CHANGELOG
doppelgangR/DESCRIPTION
doppelgangR/NAMESPACE
doppelgangR/R
doppelgangR/R/DoppelGang-class.R
doppelgangR/R/corFinder.R
doppelgangR/R/doppelgangR.R
doppelgangR/R/nonexports.R
doppelgangR/R/outer2df.R
doppelgangR/R/outlierFinder.R
doppelgangR/R/phenoDist.R
doppelgangR/R/phenoFinder.R
doppelgangR/R/smokingGunFinder.R
doppelgangR/R/sn.R
doppelgangR/R/vectorHammingDist.R
doppelgangR/R/vectorWeightedDist.R
doppelgangR/build
doppelgangR/build/partial.rdb
doppelgangR/build/vignette.rds
doppelgangR/inst
doppelgangR/inst/CRC.R
doppelgangR/inst/GSE44104.R
doppelgangR/inst/NEWS
doppelgangR/inst/RUNME.sh
doppelgangR/inst/TCGA.R
doppelgangR/inst/TCGA_microarray_RNAseq.R
doppelgangR/inst/bladder.R
doppelgangR/inst/breast.R
doppelgangR/inst/count_totals.R
doppelgangR/inst/countdops.R
doppelgangR/inst/doc
doppelgangR/inst/doc/doppelgangR.R
doppelgangR/inst/doc/doppelgangR.Rmd
doppelgangR/inst/doc/doppelgangR.html
doppelgangR/inst/knitR.R
doppelgangR/inst/make_cellline_esets.R
doppelgangR/inst/ovarian.R
doppelgangR/inst/ovc_small_datasets.R
doppelgangR/man
doppelgangR/man/DoppelGang-class.Rd
doppelgangR/man/corFinder.Rd
doppelgangR/man/doppelgangR-package.Rd
doppelgangR/man/doppelgangR.Rd
doppelgangR/man/dst.Rd
doppelgangR/man/mst.mle.Rd
doppelgangR/man/outlierFinder.Rd
doppelgangR/man/phenoDist.Rd
doppelgangR/man/phenoFinder.Rd
doppelgangR/man/plot-methods.Rd
doppelgangR/man/print-methods.Rd
doppelgangR/man/show-methods.Rd
doppelgangR/man/smokingGunFinder.Rd
doppelgangR/man/summary-methods.Rd
doppelgangR/man/vectorHammingDist.Rd
doppelgangR/man/vectorWeightedDist.Rd
doppelgangR/runinline.sh
doppelgangR/tests
doppelgangR/tests/maintest.R
doppelgangR/vignettes
doppelgangR/vignettes/doppelgangR.Rmd
doppelgangR/vignettes/manuscript
doppelgangR/vignettes/manuscript/doppelgangR.Rmd