View source: R/summarize_dataset.R
summarize_dataset | R Documentation |
Take a results list as produced by analyze_dataset and add additional entries for inter-sample and inter-locus analyses.
summarize_dataset(results, genotypes_known = NULL)
results |
list containing summary data frame and sample-specific data frames as produced by analyze_dataset. |
genotypes_known |
optional data frame of known genotypes that should be
compared to the observed genotypes in the results, as loaded by
load_genotypes. If provided |
Additional entries in the returned list:
alignments
: inter-allele alignments for each locus, from
align_alleles.
dist_mat
: inter-sample distance matrix, from make_dist_mat
.
dist_mat_known
: if genotypes_known is given, this distance matrix
of sample-to-individual values will be present, from make_dist_mat_known
.
If genotypes_known is given and a Name column is present in
results$summary
, samples will be matched with the genotypes in
genotypes_known and additional columns will be present in the summary data
frame:
CorrectAllele1Seq
: One correct allele sequence for the individual. The
order of this and CorrectAllele2Seq
will be matched to Allele1Seq
and
Allele2Seq
if possible. See match_known_genotypes.
CorrectAllele2Seq
: A second correct allele sequence, as above.
GenotypeResult
: Categorization for each entry as Correct, Incorrect,
Blank, or Dropped Allele. See categorize_genotype_results.
expanded list with additional summaries.
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