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).

AuthorLevi Waldron, Markus Riester, Marcel Ramos
Date of publicationNone
MaintainerLevi Waldron <lwaldron.research@gmail.com>
LicenseGPL (>=2.0)
Version1.2.0
https://github.com/lwaldron/doppelgangR

View on Bioconductor

Functions

corFinder Man page
DoppelGang Man page
DoppelGang-class Man page
doppelgangR Man page
doppelgangR-package Man page
dst Man page
mst.mle Man page
outlierFinder Man page
phenoDist Man page
phenoFinder Man page
plot,DoppelGang Man page
plot.DoppelGang Man page
plot,DoppelGang,ANY-method Man page
plot,DoppelGang-method Man page
plot.doppelgangR Man page
plot-methods Man page
print,DoppelGang-method Man page
print-methods Man page
pst Man page
qst Man page
rst Man page
show,DoppelGang-method Man page
show-methods Man page
smokingGunFinder Man page
st.mle Man page
summary,DoppelGang-method Man page
summary-methods Man page
vectorHammingDist Man page
vectorWeightedDist Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.