Description Usage Arguments Value Author(s) References See Also Examples
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.
1 | BADGERpredSNP(MATEXP, MATSNP, BADGEREXP=NULL)
|
MATEXP |
A numeric matrix of expression values, the columns of which correspond
to the columns of |
MATSNP |
A numeric matrix of genotype calls corresponding to |
BADGEREXP |
A numeric matrix of expression values for which corresponding genotypes
will be predicted. If NULL, values will be predicted for the |
A matrix of mode numeric containing predicted genotypes corresponding to BADGEREXP
.
Lynch AG
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/
BADGER
,BADGERmatchScores
,QTLres
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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),]
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.