impute.genotypes: Impute Sanger SNPs onto mouse genomes.

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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  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

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  ## 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.