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uqrmaie1 / admixtools

https://uqrmaie1.github.io/admixtools
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error when running extract_f2 and qpfstats set as TRUE #50

Open jaurbanChicago opened 10 months ago

jaurbanChicago commented 10 months ago

Getting this error when running extract_f2 with qpfstats as TRUE.

i Reading metadata...
i Computing block lengths for 589494 SNPs...
i Computing 3081 f4-statistics for block 549 out of 549...
i Constructing matrix...
i Running regression...
NULL
Warning messages:
1: In extract_f2("SriLanka_HONaka_ALG_posrefine.nohardfiltering.norm.onlybiallelicsnps_forqpgraph",  :
  Most `extract_f2` options will be ignored when using the `qpfstats` option!
2: In is.character(pop1) && file.exists(pop1) :
  'length(x) = 13 > 1' in coercion to 'logical(1)'
3: In is.character(pop1) && file.exists(pop1) :
  'length(x) = 13 > 1' in coercion to 'logical(1)'
4: Specifying the `id_cols` argument by position was deprecated in tidyr 1.3.0.
i Please explicitly name `id_cols`, like `id_cols = 1:4`.
i The deprecated feature was likely used in the admixtools package.
  Please report the issue at <https://github.com/uqrmaie1/admixtools/issues>.
uqrmaie1 commented 10 months ago

Those are just warnings, not errors. You can safely ignore 2-4 (I fixed the underlying causes, in the next version those warnings should be gone.) The first warning just reminds you that the qpfstats option isn't compatible with many other options to extract_f2.