doppelgangR-package {doppelgangR}R Documentation

Identify likely duplicate samples from genomic or meta-data

Description

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).

Details

The DESCRIPTION file:

Package: doppelgangR
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Depends: R (>= 3.3), Biobase, BiocParallel
Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy
Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, utils
Author: Levi Waldron, Markus Riester, Marcel Ramos
Version: 1.8.0
Date: 2017-04-25
License: GPL (>=2.0)
Title: Identify likely duplicate samples from genomic or meta-data
Description: 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).
URL: https://github.com/lwaldron/doppelgangR
BugReports: https://github.com/lwaldron/doppelgangR/issues
VignetteBuilder: knitr
biocViews: RNASeq, Microarray, GeneExpression, QualityControl
NeedsCompilation: no

Index of help topics:

DoppelGang-class        DoppelGang S4 class
corFinder               Calculate pair-wise correlations between
                        samples using the expr() slots of a list of two
                        ExpressionSets.
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 distribution
outlierFinder           Identifies outliers in a similarity matrix.
phenoDist               Calculate distance between two vectors, rows of
                        one matrix/dataframe, or rows of two
                        matrices/dataframes.
phenoFinder             Calculate pairwise similarities of phenoData
                        between samples for a list containing two
                        ExpressionSets
plot-methods            Histograms of all pairwise sample correlations,
                        showing identified doppelgangers.
print-methods           Print a DoppelGang object
show-methods            Show a DoppelGang object
smokingGunFinder        Find doppelgangers based on "smoking gun"
                        phenotypes - those that should be unique to
                        each patient.
summary-methods         Summarizes a DoppelGang object
vectorHammingDist       Calculate Hamming Distance between two vectors,
                        using pairwise complete observations.
vectorWeightedDist      Calculate a weighted distance between two
                        vectors, using pairwise complete observations.

Author(s)

Levi Waldron, Markus Riester, Marcel Ramos

Maintainer: Levi Waldron <lwaldron.research@gmail.com>


[Package doppelgangR version 1.8.0 Index]