Create snp information table for a cross
Create a table of snp information from a cross, for use with scan1snps()
.
create_snpinfo(cross)
cross |
Object of class |
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.
## 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") ## End(Not run)
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