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doppelgangR (version 1.0.2)

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).

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Version

Version

1.0.2

License

GPL (>=2.0)

Issues

0

Pull Requests

0

Stars

5

Forks

4

Maintainer

Levi Waldron

Last Published

February 15th, 2017

Functions in doppelgangR (1.0.2)

DoppelGang-class

DoppelGang S4 class
plot-methods

Histograms of all pairwise sample correlations, showing identified doppelgangers.
print-methods

Print a DoppelGang object
dst

Skew-t Distribution
phenoDist

Calculate distance between two vectors, rows of one matrix/dataframe, or rows of two matrices/dataframes.
summary-methods

Summarizes a DoppelGang object
outlierFinder

Identifies outliers in a similarity matrix.
vectorWeightedDist

Calculate a weighted distance between two vectors, using pairwise complete observations.
mst.mle

Maximum likelihood estimation for a (multivariate) skew-t distribution
doppelgangR

doppelgangR
corFinder

Calculate pair-wise correlations between samples using the expr() slots of a list of two ExpressionSets.
vectorHammingDist

Calculate Hamming Distance between two vectors, using pairwise complete observations.
phenoFinder

Calculate pairwise similarities of phenoData between samples for a list containing two ExpressionSets
doppelgangR-package

Identify likely duplicate samples from genomic or meta-data
show-methods

Show a DoppelGang object
smokingGunFinder

Find doppelgangers based on "smoking gun" phenotypes - those that should be unique to each patient.