Find name of indexed snp
For a particular SNP, find the name of the corresponding indexed SNP.
find_index_snp(snpinfo, snp)
snpinfo |
Data frame with SNP information with the following columns:
|
snp |
Name of snp to look for (can be a vector). |
A vector of SNP IDs (the corresponding indexed SNPs), with NA if a SNP is not found.
## Not run:
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/master/DO_Recla/recla.zip")
recla <- read_cross2(file)
# founder genotypes for a set of SNPs
snpgeno <- rbind(m1=c(3,1,1,3,1,1,1,1),
m2=c(3,1,1,3,1,1,1,1),
m3=c(1,1,1,1,3,3,3,3),
m4=c(1,3,1,3,1,3,1,3))
sdp <- calc_sdp(snpgeno)
snpinfo <- data.frame(chr=c("19", "19", "X", "X"),
pos=c(40.36, 40.53, 110.91, 111.21),
sdp=sdp,
snp=c("m1", "m2", "m3", "m4"), stringsAsFactors=FALSE)
# update snp info by adding the SNP index column
snpinfo <- index_snps(recla$pmap, snpinfo)
# find indexed snp for a particular snp
find_index_snp(snpinfo, "m3")
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