genoprob_to_snpprob: Convert genotype probabilities to SNP probabilities
In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description Usage Arguments Details Value See Also Examples

For multi-parent populations, convert use founder genotypes at a set of SNPs to convert founder-based genotype probabilities to SNP genotype probabilities.

1	genoprob_to_snpprob(genoprobs, snpinfo)

genoprobs

Genotype probabilities as calculated by qtl2geno::calc_genoprob().

snpinfo

Data frame with SNP information with the following columns (the last three are generally derived with index_snps()):

chr - Character string or factor with chromosome
pos - Position (in same units as in the "map" attribute in genoprobs.
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
snp - Character string with SNP identifier (if missing, the rownames are used).
index - Indices that indicate equivalent groups of SNPs, calculated by index_snps().
intervals - Indexes that indicate which marker intervals the SNPs reside.
on_map - Indicate whether SNP coincides with a marker in the genoprobs

We first split the SNPs by chromosome and use snpinfo$index to subset to non-equivalent SNPs. snpinfo$interval indicates the intervals in the genotype probabilities that contain each. For SNPs contained within an interval, we use the average of the probabilities for the two endpoints. We then collapse the probabilities according to the strain distribution pattern.

An object like the genoprobs input, but with imputed genotype probabilities at the selected SNPs indicated in snpinfo$index.

If the input genoprobs is for allele probabilities, the probs output has just two probability columns (for the two SNP alleles). If the input has a full set of n(n+1)/2 probabilities for n strains, the probs output has 3 probabilities (for the three SNP genotypes). If the input has full genotype probabilities for the X chromosome (n(n+1)/2 genotypes for the females followed by n hemizygous genotypes for the males), the output has 5 probabilities: the 3 female SNP genotypes followed by the two male hemizygous SNP genotypes.

index_snps(), qtl2geno::calc_genoprob(), scan1snps()

## Not run: 
# load example data and calculate genotype probabilities
library(qtl2geno)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/DO_Recla/recla.zip")
recla <- read_cross2(file)
recla <- recla[c(1:2,53:54), c("19","X")] # subset to 4 mice and 2 chromosomes
probs <- calc_genoprob(recla, error_prob=0.002)

# founder genotypes for a set of SNPs
snpgeno <- rbind(m1=c(3,1,1,3,1,1,1,1),
                 m2=c(1,3,1,3,1,3,1,3),
                 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)

# identify groups of equivalent SNPs
snpinfo <- index_snps(recla$pmap, snpinfo)

# collapse to SNP genotype probabilities
snpprobs <- genoprob_to_snpprob(probs, snpinfo)

# could also first convert to allele probs
aprobs <- genoprob_to_alleleprob(probs)
snpaprobs <- genoprob_to_snpprob(aprobs, snpinfo)

## End(Not run)