qtl2 (version 0.32)

create_snpinfo: Create snp information table for a cross

Description

Create a table of snp information from a cross, for use with scan1snps().

Usage

create_snpinfo(cross)

Value

A data frame of SNP information with the following columns:

• chr - Character string or factor with chromosome

• pos - Position (in same units as in the "map" attribute in genoprobs.

• snp - Character string with SNP identifier (if missing, the rownames are used).

• sdp - Strain distribution pattern: an integer, between 1 and \(2^n - 2\) where \(n\) is the number of strains, whose binary encoding indicates the founder genotypes SNPs with missing founder genotypes are omitted.

Arguments

cross

Object of class "cross2". For details, see the R/qtl2 developer guide.

See Also

index_snps(), scan1snps(), genoprob_to_snpprob()

Examples

if (FALSE) {
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DO_Recla/recla.zip")
recla <- read_cross2(file)
snpinfo <- create_snpinfo(recla)

# calculate genotype probabilities
pr <- calc_genoprob(recla, error_prob=0.002, map_function="c-f")

# index the snp information
snpinfo <- index_snps(recla$pmap, snpinfo)

# sex covariate
sex <- setNames((recla$covar$Sex=="female")*1, rownames(recla$covar))

# perform a SNP scan
out <- scan1snps(pr, recla$pmap, recla$pheno[,"bw"], addcovar=sex, snpinfo=snpinfo)

# plot the LOD scores
plot(out$lod, snpinfo, altcol="green3")
}