qtl2 (version 0.24)

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)

Arguments

cross

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

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.

See Also

index_snps(), scan1snps(), genoprob_to_snpprob()

Examples

# 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)
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")
# }
# NOT RUN {
# }