exampleSNP: Example genotype matrix for the BADGER package.

Description Usage Format Source References Examples

Description

A matrix of 420 genotype callsfor 81 individuals.

Usage

1

Format

The format is: num [1:420, 1:81] 1 1 1 1 1 2 2 2 2 2 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:81] "NA18500" "NA18501" "NA18503" "NA18504" ...

Source

http://hapmap.ncbi.nlm.nih.gov/biomart/martview/

References

Westra HJ et al. (2011) MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics 27: 2104-2111. Stranger BE et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (New York, NY) 315: 848-853.

Examples

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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.