BADGER-package: A package for identifying sample mixups in combined...

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

Description

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.

Details

Package:	BADGER
Type:	Package
Version:	1.0
Date:	2012-06-21
License:	GPL-2

BADGERpredSNP takes two matrices, one expression and one genotype, the rows of which correspond to eQTLs. From these, it estimates the nature of the eQTL-like relationships, and makes predictions of genotype either for the given expression matrix or an additional expression matrix

Author(s)

Lynch, AG

References

Lynch et al. "Ensuring data integrity in large modern integrative genomic studies" ECCB 2010, Ghent, Poster abstract. http://www.ebi.ac.uk/eccb/2010/index.php/proceedings/posters/122-other-bioinformatics-applications.html

Curtis et al. "The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups" Nature 486, 346-352

Lynch et al. "Calling sample mixups in cancer population studies" submitted

Examples

data(exampleEXP)
data(exampleSNP)
mysampnames<-sapply(colnames(exampleEXP),function(x){unlist(strsplit(as.character(x),"_"))[2]})
mypred<-BADGERpredSNP(exampleEXP[,match(colnames(exampleSNP),mysampnames)],exampleSNP,exampleEXP)
myQTLres<-QTLres(mypred[,match(colnames(exampleSNP),mysampnames)],exampleSNP)
myMS<-BADGERmatchScores(mypred,exampleSNP,which(myQTLres<35))

mycheck<-rep(0,422) 
for(i in 1:422){mycheck[i]<-colnames(exampleSNP)[which.min(myMS[i,])]} 
mycheck[!(mysampnames %in% colnames(exampleSNP))]<-NA

# see that there is a problem with the expression matrices associated with NA18515

cbind(mycheck,mysampnames)[which(mycheck!=mysampnames),]

BADGER documentation built on May 2, 2019, 4:56 p.m.