BADGERpredSNP: Function to predict genotypes from an expression matrix

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

Description

Given two matrices (one of expression values and one of genotype calls), ordered by a set of known or suspected eQTLs, this function defines the nature of those eQTL relationship and predicts genotypes from a third matrix of expression values.

Usage

BADGERpredSNP(MATEXP, MATSNP, BADGEREXP=NULL)

Arguments

MATEXP	A numeric matrix of expression values, the columns of which correspond to the columns of MATSNP (i.e. supposedly from the same sample). The rows of MATEXP are believed to correspond to the rows of MATSNP via an eQTL.
MATSNP	A numeric matrix of genotype calls corresponding to MATEXP as described above.
BADGEREXP	A numeric matrix of expression values for which corresponding genotypes will be predicted. If NULL, values will be predicted for the MATEXP matrix.

Value

A matrix of mode numeric containing predicted genotypes corresponding to BADGEREXP.

Author(s)

Lynch AG

References

First used/described in

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

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

See Also

BADGER,BADGERmatchScores,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.