create_snpinfo {qtl2} | R Documentation |
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 |
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 ingenoprobs
. -
snp
- Character string with SNP identifier (if missing, the rownames are used). -
sdp
- Strain distribution pattern: an integer, between 1 and2^n - 2
wheren
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/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")
## End(Not run)
[Package qtl2 version 0.36 Index]