The dcifer tutorial needs to be fixed:
- data wrangling is incorrect, VCF outputs read counts at the moment but should be genotypes (this also relates to the PGEhammer
vcf2long() update)
- the
dsmp object is not created in the tutorial, so the tutorial uses the data from the dcifer package to calculate COI and allele frequencies instead of the PGEforge VCF that is read in
|
coi <- getCOI(dsmp, lrank = lrank) |
|
afreq <- calcAfreq(dsmp, coi, tol = 1e-5) |
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dres0 <- ibdDat(dsmp, coi, afreq, pval = TRUE, confint = TRUE, rnull = 0, |
The dcifer tutorial needs to be fixed:
vcf2long()update)PGEforge/tutorials/dcifer/dcifer_analysis.Rmd
Line 43 in f289828
dsmpobject is not created in the tutorial, so the tutorial uses the data from thedciferpackage to calculate COI and allele frequencies instead of the PGEforge VCF that is read inPGEforge/tutorials/dcifer/dcifer_analysis.Rmd
Line 55 in f289828
PGEforge/tutorials/dcifer/dcifer_analysis.Rmd
Line 61 in f289828
PGEforge/tutorials/dcifer/dcifer_analysis.Rmd
Line 66 in f289828