[R-sig-genetics] [R-sig-phylo] PEGAS: why did pegas not assign separate haplotype
Emmanuel Paradis
emm@nue|@p@r@d|@ @end|ng |rom |rd@|r
Wed Mar 4 17:06:00 CET 2020
Hi Hirra,
I've tried with the data you pisted below using pegas 0.12 and I was not able to repeat your results: I found that seqs. 1 and 3 are grouped in the same haplotype (not 1 and 2). Anyway, this is the same issue that you pointed out a few days ago: seq. 3 could be grouped with seq. 1 or seq. 2. I have now implemented the changes I described in my previous message, and have just pushed pegas 0.12-999 on GitHub. This also include changes to make pegas work with R 4.0.0 (see the results of R CMD check on CRAN for details). This new version will be submitted to CRAN in a few days as pegas 0.13. In the meantime, don't hesitate to try this new version!
Best,
Emmanuel
----- Le 3 Mar 20, à 21:00, Hirra Farooq hirra.farooq using postgrad.manchester.ac.uk a écrit :
> Hello,
>
> I have a question about the pegas haplotype algorithm and would be grateful if
> someone could explain.
>
> I used pegas haplotype() on a set of sequences. I then manually aligned and
> looked at the sequences within each haplotype. For one haplotype I noticed
> something odd (see image below)
>
> Although there was a single bp difference at the highlighted position ,these
> sequences had all been assigned as one haplotype. I understand that for the 3rd
> sequence because there are gaps at this highlighted position this can lead it
> to be pooled with others, but I do not understand how sequence 1 and 2 can be
> in the same haplotype?
>
> I would be grateful for any guidance,
>
>
>
>
>
>
> GBSP11539-19|Ophlitaspon[1]
> AATACTGCATTTTTTGACCCTGCAGGGGGAGGAGACCCCATTTTATATCAACATTTATTT 660
> GBSP11518-19|Ophlitaspon[2]
> AATACTGCATTTTTTGACCCTGCGGGGGGAGGAGACCCCATTTTA--------------- 645
> GBSP11504-19|Ophlitaspon[3]
> AATACTGCAT-------------------------------------------------- 580
> GBSP11512-19|Ophlitaspon[4]
> AATACTGCATTTTTTGACCCTGCAGGGGGAGGAGACCCATTTATATCACTTTATTTGTT- 659
> **********
>
> Best wishes
> Hirra
> University of Manchester Student.
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-phylo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
More information about the R-sig-genetics
mailing list