impute.genotypes {DOQTL} | R Documentation

## 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")

### 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)

[Package DOQTL version 1.16.2 Index]