find_index_snp: Find name of indexed snp

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Find name of indexed snp

Description

For a particular SNP, find the name of the corresponding indexed SNP.

Usage

find_index_snp(snpinfo, snp)

Arguments

snpinfo	Data frame with SNP information with the following columns: chr - Character string or factor with chromosome index - Numeric index of equivalent, indexed SNP, as produced by index_snps(). snp - Character string with SNP identifier (if missing, the rownames are used).
snp	Name of snp to look for (can be a vector).

Value

A vector of SNP IDs (the corresponding indexed SNPs), with NA if a SNP is not found.

See Also

find_marker()

Examples

## Not run: 
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/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")

## End(Not run)

qtl2 documentation built on May 29, 2024, 11:46 a.m.