| doppelgangR-package {doppelgangR} | R Documentation |
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).
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.
Levi Waldron, Markus Riester, Marcel Ramos
Maintainer: Levi Waldron <lwaldron.research@gmail.com>