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get_solcap_snp_pos.R not assigning markers per sequence #67

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wrengs opened this issue Oct 11, 2023 · 0 comments
Open

get_solcap_snp_pos.R not assigning markers per sequence #67

wrengs opened this issue Oct 11, 2023 · 0 comments

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@wrengs
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wrengs commented Oct 11, 2023

Dear Marcello,

Following the MAPpoly workhshop for potato ( https://www.youtube.com/watch?v=NifLfBsQshQ ), I am running into issues whereby the get_solcap_snp_pos.R does not assign genome position e.g. number of markers per chromosome as done within the workshop.

print(dat, detailed = T) gives the same output before and after running source("get_solcap_snp_pos.R")

This is an object of class 'mappoly.data'
    Ploidy level:                            4 
    No. individuals:                         156 
    No. markers:                             6531 
    Prob. threshold to declare missing:      0.95 
    Missing data:                            5.26%
    Redundant markers:                       7.92%

    No. markers per chromosome: not available
    ----------
    No. of markers per dosage combination in both parents:
    P1 P2 freq
     0  1  191
     0  2   74
     0  3   29
     1  0  526
     1  1  634
     1  2  379
     1  3  146
     1  4   51
     2  0  167
     2  1  431
     2  2  739
     2  3  538
     2  4  238
     3  0   34
     3  1  162
     3  2  402
     3  3  743
     3  4  658
     4  1   28
     4  2  112
     4  3  249

Given the time difference between my question and the workshop, I am inclined to think it might be a slight difference in potential language invoked by R due to updates. Additionally, there is a difference between mappoly packages used in the workshop (MAPpoly v0.2.1) and the current version (MAPpoly v0.3.3).
I am running R v4.3.1 (2023-06-16)

As the issue has not yet been described here, I was hoping you could provide some insights.

Many thanks in advance!

Kind regards,
Willem

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