DOQTL (version 1.8.0)

impute.genotypes: Impute Sanger SNPs onto mouse genomes.

Description

Given a GRanges object containing a single range on one chromosome and haplotype probabilities, impute the Sanger SNPs onto the DO genomes.

Usage

impute.genotypes(gr, probs, markers, vcf.file, hq = TRUE,  cross = c("DO", "CC", "DOF1", "HS", "HSrat", "other"))

Arguments

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")

Value

A file written out to the outfile name.

Details

This function takes the mean of the haplotype probabilities between two markers and does not linearly interpolate between markers.

Examples

  ## Not run: 
#     impute.genotypes(gr, probs, markers, vcf.file, hq = TRUE, 
#     cross = "DO")
#   ## End(Not run)