doppelgangR: Identify likely duplicate samples from genomic or meta-data
Version 1.4.1

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
Bioconductor views GeneExpression Microarray QualityControl RNASeq
Date of publicationNone
MaintainerLevi Waldron <lwaldron.research@gmail.com>
LicenseGPL (>=2.0)
Version1.4.1
URL https://github.com/lwaldron/doppelgangR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("doppelgangR")

Getting started

Package overview
doppelgangR

Popular man pages

corFinder: Calculate pair-wise correlations between samples using the...
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...
smokingGunFinder: Find doppelgangers based on "smoking gun" phenotypes - those...
vectorHammingDist: Calculate Hamming Distance between two vectors, using...
See all...

All man pages Function index File listing

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...

Functions

DoppelGang Man page
DoppelGang-class Man page
Owen Source code
checkSameEsets Source code
corFinder Man page Source code
cp.to.dp Source code
discretizeDataFrame Source code
dmsn Source code
dmst Source code
doppelgangR Man page
doppelgangR-package Man page
dp.to.cp Source code
dsn Source code
dsn2.plot Source code
dst Man page Source code
dst2.plot Source code
gamma1.to.lambda Source code
getMatrixPair Source code
log.pt Source code
msn.affine Source code
msn.cond.plot Source code
msn.conditional Source code
msn.dev Source code
msn.dev.grad Source code
msn.fit Source code
msn.marginal Source code
msn.mle Source code
msn.moment.fit Source code
msn.quantities Source code
mst.affine Source code
mst.dev Source code
mst.dev.grad Source code
mst.fit Source code
mst.mle Man page Source code
num.deriv1 Source code
num.deriv2 Source code
outer2df Source code
outlierFinder Man page Source code
phenoDist Man page
phenoFinder Man page Source code
plot,DoppelGang Man page
plot,DoppelGang,ANY-method Man page
plot,DoppelGang-method Man page
plot-methods Man page
plot.DoppelGang Man page
plot.doppelgangR Man page
pmsn Source code
pmst Source code
print,DoppelGang-method Man page
print-methods Man page
psn Source code
pst Man page Source code
qsn Source code
qst Man page Source code
rmsn Source code
rmst Source code
rsn Source code
rst Man page Source code
sample.centralmoments Source code
show,DoppelGang-method Man page
show-methods Man page
smokingGunFinder Man page Source code
sn.2logL.profile Source code
sn.Einfo Source code
sn.SFscore Source code
sn.cumulants Source code
sn.dev Source code
sn.dev.gh Source code
sn.em Source code
sn.logL.grouped Source code
sn.mle Source code
sn.mle.grouped Source code
sn.mmle Source code
solvePD Source code
st.2logL.profile Source code
st.SFscore Source code
st.cumulants Source code
st.cumulants.inversion Source code
st.dev.fixed Source code
st.logL.grouped Source code
st.mle Man page Source code
st.mle.grouped Source code
st.mmle Source code
summary,DoppelGang-method Man page
summary-methods Man page
vectorHammingDist Man page
vectorWeightedDist Man page Source code
zeta Source code

Files

CHANGELOG
DESCRIPTION
NAMESPACE
R
R/DoppelGang-class.R
R/corFinder.R
R/doppelgangR.R
R/nonexports.R
R/outer2df.R
R/outlierFinder.R
R/phenoDist.R
R/phenoFinder.R
R/smokingGunFinder.R
R/sn.R
R/vectorHammingDist.R
R/vectorWeightedDist.R
build
build/partial.rdb
build/vignette.rds
inst
inst/CITATION
inst/CRC.R
inst/GSE44104.R
inst/NEWS
inst/RUNME.sh
inst/TCGA.R
inst/TCGA_microarray_RNAseq.R
inst/bladder.R
inst/breast.R
inst/count_totals.R
inst/countdops.R
inst/doc
inst/doc/doppelgangR.R
inst/doc/doppelgangR.Rmd
inst/doc/doppelgangR.html
inst/knitR.R
inst/make_cellline_esets.R
inst/ovarian.R
inst/ovc_small_datasets.R
man
man/DoppelGang-class.Rd
man/corFinder.Rd
man/doppelgangR-package.Rd
man/doppelgangR.Rd
man/dst.Rd
man/mst.mle.Rd
man/outlierFinder.Rd
man/phenoDist.Rd
man/phenoFinder.Rd
man/plot-methods.Rd
man/print-methods.Rd
man/show-methods.Rd
man/smokingGunFinder.Rd
man/summary-methods.Rd
man/vectorHammingDist.Rd
man/vectorWeightedDist.Rd
runinline.sh
tests
tests/maintest.R
vignettes
vignettes/doppelgangR.Rmd
vignettes/manuscript
vignettes/manuscript/doppelgangR.Rmd
doppelgangR documentation built on May 20, 2017, 10:14 p.m.

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