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>