Hello,
Emmanuel Paradis has recently updated the haplotype() function in pegas
0.13 to account for base ambiguities, gaps and Ns. Thank you Emmanuel!
The argument 'strict' simply considers or ignores all gaps and
ambiguities, but does this also consider/ignore Ns?
The 'trailingGapsAsN' simply treats leading and trailing gaps as Ns,
ignoring internal gaps. This argument is set to TRUE by default.
>From the above, it appears that 'strict' ignores Ns. If 'strict' is set to
TRUE, does this mean that TRUE/FALSE assignment 'trailingGapsAsN' is ignored
as well?
The reason I ask is because I use haplotype() in one of my R packages to
compute optimal sample sizes for genetic diversity assessment (HACSim).
Currently in my package, R throws a warning to users if missing data or
base ambiguities are present within DNA alignments.
Given Emmanuel's changes, it seems the warning in my package will not be
needed once I set 'strict = TRUE'. I am unsure however on how to properly
set 'trailingGapsAsN' to ensure that gaps do not affect haplotype
calculation if they are left in the alignment. Gaps, ambiguities and Ns
will cause an overestimation of haplotypes, and therefore an inflation of
standing genetic variation.
Can someone weigh in on this?
Thanks!
Cheers,
Jarrett
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