BADGERmatchScores: Function to compare matrices of predicted and observed...

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

Description

This function compares the predicted genotypes from n expression arrays, and compares them to m observed genotype arrays.

Usage

BADGERmatchScores(predictedSNP, BADGERSNP, useEQTL = NULL)

Arguments

predictedSNP	numeric matrix of g predicted genotypes (probably from BADGERpredSNP) from n expression arrays.
BADGERSNP	numeric matrix of g observed genotypes from m SNP arrays.
useEQTL	which of the g genotypes should contribute? (NULL = all)

Value

a numeric n x m matrix containing a score for the comparison of each SNP array with each expression array

Author(s)

Lynch AG

References

First used/described in

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

Curtis et al. 2012 "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

http://badger.r-forge.r-project.org/

See Also

BADGER,BADGERpredSNP,QTLres

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.