impute.genotypes: Impute Sanger SNPs onto mouse genomes.

In DOQTL: Genotyping and QTL Mapping in DO Mice

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")

Details

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

Value

A file written out to the outfile name.

Author(s)

Daniel Gatti

Examples

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

DOQTL documentation built on May 6, 2019, 3:09 a.m.