BADGER: A package for identifying sample mixups in combined expression and genotyping studies.

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BADGER takes a set of expression array data and one of genotype array data and, given information on how sample mappings were intended to be, determines the apparent relationships between genotype and expression before predicting genotypes for each expression array. From these predictions, mismatches can be identified.

Author
Lynch AG, Dunning MJ
Date of publication
None
Maintainer
AG Lynch <andy.lynch@cancer.org.uk>
License
GPL-2
Version
1.0

View on R-Forge

Man pages

BADGERmatchScores
Function to compare matrices of predicted and observed...
BADGER-package
A package for identifying sample mixups in combined...
BADGERpredSNP
Function to predict genotypes from an expression matrix
exampleEXP
Example expression matrix for the BADGER package.
exampleSNP
Example genotype matrix for the BADGER package.
QTLres
Function to assess the performance of the eQTLs that BADGER...

Files in this package

BADGER
BADGER/data
BADGER/data/exampleEXP.rda
BADGER/data/exampleSNP.rda
BADGER/R
BADGER/R/BADGERmatchScores.R
BADGER/R/QTLres.R
BADGER/R/BADGERpredSNP.R
BADGER/NAMESPACE
BADGER/DESCRIPTION
BADGER/man
BADGER/man/BADGERpredSNP.Rd
BADGER/man/BADGERmatchScores.Rd
BADGER/man/QTLres.Rd
BADGER/man/exampleSNP.Rd
BADGER/man/exampleEXP.Rd
BADGER/man/BADGER-package.Rd