cc.trans.probs


    Character vector containing the two letter codes (i.e. AA, BB, CC, etc.) for the homozygous states.
  

states


    Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. <em>Not required for DO.</em>
  

snps


    Character containing the chromosome.
  


    Character that is either M or FALSE, indicating the sex to use. Only relevant on X chromosome.
  


  Thie function returns the transition probabilities for fully inbred Collaborative Cross mice.


 transition 

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Daniel Gatti

DOQTL

Genotyping and QTL Mapping in DO Mice

cc.trans.probs function

Character vector containing the two letter codes (i.e. AA, BB, CC, etc.) for the homozygous states.

Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. <em>Not required for DO.</em>

Character that is either M or FALSE, indicating the sex to use. Only relevant on X chromosome.

Thie function returns the transition probabilities for fully inbred Collaborative Cross mice.

cc.trans.probs: Transition probabilities for CC mice.

Description

Usage

Arguments

Value

Details

References

Examples