simu

<p></p><p>  The data obtained by <code>simulateForFabia</code> in binary format.
  
</p>

datasets

A package to identify very short IBD segments in large
sequencing data by FABIA biclustering. Two haplotypes are
identical by descent (IBD) if they share a segment that both
inherited from a common ancestor. Current IBD methods reliably
detect long IBD segments because many minor alleles in the
segment are concordant between the two haplotypes. However,
many cohort studies contain unrelated individuals which share
only short IBD segments. This package provides software to
identify short IBD segments in sequencing data. Knowledge of
short IBD segments are relevant for phasing of genotyping data,
association studies, and for population genetics, where they
shed light on the evolutionary history of humans. The package
supports VCF formats, is based on sparse matrix operations, and
provides visualization of haplotype clusters in different
formats.

Sepp Hochreiter

hapFabia

hapFabia: Identification of very short segments of identity by
descent (IBD) characterized by rare variants in large
sequencing data

simu function

contains a list <code>simu</code> with  variables
  <ol>
<li> <code>namesL</code>,
    </li>
<li> <code>haploN</code>,
    </li>
<li> <code>snvs</code>,
    </li>
<li> <code>annot</code>,
    </li>
<li> <code>alleleIimp</code> which contains the information on the
    implanted IBD segment: sample names,
  number of chromosomes/individuals,
  number of tagSNVs, annotation of tagSNVs, the genotype data
  where 0 = reference an 1 = minor allele.
</li>
</ol> <code>annot</code> is a list with entries:
  <ol>
<li> <code>chromosome</code>, 
   </li>
<li> <code>position</code>,
   </li>
<li> <code>snvNames</code>,  
   </li>
<li> <code>snvMajor</code>,  
   </li>
<li> <code>snvMinor</code>,  
   </li>
<li> <code>quality</code>,   
   </li>
<li> <code>pass</code>,     
   </li>
<li> <code>info</code>,      
   </li>
<li> <code>fields</code>,    
   </li>
<li> <code>frequency</code>, and 
   </li>
<li> <code>changed</code>.
 </li>
</ol> 

Format

Source

The data obtained by <code>simulateForFabia</code> in binary format.

simu: Example simulation data for `hapFabia`

Description

Usage

Arguments

Format

Source

References

See Also