impute.genotypes {DOQTL} | R Documentation |
Given a GRanges object containing a single range on one chromosome and haplotype probabilities, impute the Sanger SNPs onto the DO genomes.
impute.genotypes(gr, probs, markers, vcf.file, hq = TRUE, cross = c("DO", "CC", "DOF1", "HS", "HSrat", "other"))
gr |
object that contains the genomic range in which to impute SNPs. For now, this must be a single, continuous range. |
probs |
3D numeric array containing the haplotype probabilities. samples x 8 founders x markers. All dimensions must be contain dimnames. |
markers |
data.frame containing at least 3 columns that include the marker ID, chr and postion of each marker. nrow must be the same as dim(probs)[3] and markers[,1] must equal dimnames(probs)[[3]]. |
vcf.file |
String containing the full path to the Sanger SNP VCF file. |
hq |
Boolean indicating whether to use only high quality SNPs. Default = TRUE. |
cross |
Character string that is the cross type. One of "DO", "CC", "DOF1", "HS", "HSrat", "other") |
This function takes the mean of the haplotype probabilities between two markers and does not linearly interpolate between markers.
A file written out to the outfile name.
Daniel Gatti
## Not run: impute.genotypes(gr, probs, markers, vcf.file, hq = TRUE, cross = "DO") ## End(Not run)