orderSNVs: Order SNVs
In perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data
Description
Usage
Arguments
Details
Value
References
See Also
Examples
Description
This function orders the SNVs in the window around the SNV.
Usage
1
orderSNVs(snvWin)
Arguments
snvWin
See the arguments in buildDend
Details
Following Gusfield (1991), the first step in building the dendogram is to order compatible SNVs by
their ancestry. Then, following Mailund et al. (2006) the incompatible SNVs are ordered according
to their proximity to the focal SNV.
Value
A hapMat with ordered SNVs.
References
Gusfield, D. (1991). Efficient algorithms for inferring evolutionary trees.
Networks, 21(1), 19-28.
Mailund, T., Besenbacher, S., & Schierup, M. H. (2006). Whole genome association
mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics, 7(1),
454.
See Also
Examples
1
perfectphyloR documentation built on March 8, 2021, 9:06 a.m.
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Description Usage Arguments Details Value References See Also Examples
Description
This function orders the SNVs in the window around the SNV.
Usage
1 | orderSNVs(snvWin)
|
Arguments
snvWin |
See the arguments in |
Details
Following Gusfield (1991), the first step in building the dendogram is to order compatible SNVs by their ancestry. Then, following Mailund et al. (2006) the incompatible SNVs are ordered according to their proximity to the focal SNV.
Value
A hapMat with ordered SNVs.
References
Gusfield, D. (1991). Efficient algorithms for inferring evolutionary trees. Networks, 21(1), 19-28.
Mailund, T., Besenbacher, S., & Schierup, M. H. (2006). Whole genome association mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics, 7(1), 454.
See Also
Examples
1 |
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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