Reads an uploaded long-format marker genotype file (D1 format: id,
locus, allele1, allele2), validates and pivots it
(checkSequenceGenotypeFile, which applies the
checkMarkerGenotypeFile checks plus a literal-"." rejection
and a maxLoci warning, then
buildMarkerGenotypeMatrix; the Center B upload is validated
the same way),
estimates marker-based kinship independent of pedigree
(markerKinship), and surfaces a per-animal comparison of
pedigree-based mean kinship (indivMeanKin, already computed
upstream and passed in via kinshipMatrix) alongside the new
marker-based mean kinship (markerMeanKin) – an independent check
on the pedigree-implied relatedness, not a replacement for it. A second
tab surfaces the heterozygosity diagnostic: per-animal observed
heterozygosity (markerObservedHeterozygosity) alongside
population-level expected heterozygosity
(markerExpectedHeterozygosity). A third tab surfaces the
Mendelian-exclusion parentage diagnostic
(markerParentageExclusion): the pedigree's recorded
dam/sire cross-referenced against the uploaded genotypes, flagging any
recorded parent the genotype evidence contradicts. A fourth tab, "Cross-
Center", surfaces a between-population differentiation statistic
(markerFst) between the first uploaded file (implicitly
"Center A") and a second, independently uploaded Center B genotype file
– a population-level, two-dataset comparison, unrelated to the
per-animal cross-center identity linking of
resolveCrossCenterIds (Slice 4). A fifth tab, "Candidate
Parent Assignment" (issue #147 Slice 2), surfaces
markerParentageLikelihood: for every (offspring, role) pair
the Parentage Exclusion tab's own diagnostic flags as Mendelian
-inconsistent, it ranks candidate replacement parents by a CERVUS-style
multilocus likelihood (LOD) score. This tab needs no new file input –
it reads the same uploaded genotype file and pedigree already
wired to the other tabs – and is report-only, matching the Parentage
Exclusion tab's own precedent: it never writes to pedigree.
Arguments
- id
character vector of length 1. Module namespace identifier.
- kinshipMatrix
reactive returning the full pedigree-based kinship matrix (row and column names are animal IDs), or
NULLwhile upstream analysis has not yet been run.- pedigree
reactive returning the current pedigree data frame (columns
id,sire,dam), orNULLwhile upstream analysis has not yet been run.
Value
A named list of reactive elements: markerGenotype, the
raw uploaded genotype data frame (or NULL before upload);
markerKinshipMatrix, the marker-based id x id
kinship matrix (or NULL); comparisonTable, the per-animal
indivMeanKin/markerMeanKin comparison data frame (or
NULL; indivMeanKin is NA for every row when the
pedigree kinship matrix is NULL or errors, and for any genotyped
id absent from it); heterozygosityTable, the per-animal
ho/he heterozygosity data frame (he is the
population-wide mean expected heterozygosity, repeated per row) (or
NULL); exclusionTable, the
markerParentageExclusion data frame: one row per recorded
dam/sire pair with exclusionCount, nLoci and a
flagged column (TRUE where the count exceeds the
tolerance), so pairs that are not flagged are included (or
NULL before a genotype file and a pedigree are both available);
crossCenterGenotypeB, the raw uploaded Center B genotype data
frame (or NULL before upload); crossCenterTable, the
markerFst locus/fst data frame with a
trailing "Pooled" row (or NULL before both center files
are uploaded); candidateAssignmentTable, the
markerParentageLikelihood ranked-candidate data frame (a
zero-row, full-column-shape data frame when no pair is flagged; or
NULL before a genotype file and a pedigree are both available);
isReady, TRUE once comparisonTable has a value;
locusMetadataTable, the checkLocusMetadata output
(or NULL before a locus-metadata file is uploaded);
realizedRelatednessTable, the
markerRealizedRelatednessVariance output (or NULL
before pedigree/kinshipMatrix are both available);
ldBlockTable, the markerLdBlock output (or
NULL before a genotype file and a locus-metadata file are both
uploaded, or before a pedigree is available if the founders-only
restriction is checked); ldBlockExportTable, the
obfuscateLdBlocks-de-identified export preview (or
NULL before "Generate De-Identified Export Preview" is clicked
with both ldBlockTable and pedigree available);
ldBlockExportConfirmed, FALSE until the confirm-gate
modal's own Confirm button is clicked for the current export preview;
sequenceRohTable, the computeGenomicROH output (or
NULL before a genotype file and a locus-metadata file are both
uploaded, or while a threshold input is invalid);
sequenceExportGenotypeMatrix, sequenceExportRohTable
and sequenceExportManifest, the de-identified genotype matrix,
de-identified F_ROH table and export manifest captured at
"Generate De-Identified Export Preview" (each NULL before
then, and when any genotype id is absent from the pedigree or the ROH
table or pedigree is NULL); sequenceExportConfirmed,
FALSE until that
export's confirm-gate modal is accepted for the current preview;
mhcHaplotypeSummaryTable, the mhcHaplotypeFrequency
summary data frame (or NULL before an MHC haplotype file
is uploaded, or while a rarity threshold is invalid);
mhcHaplotypeCarrierTable, the mhcHaplotypeCarriers
rare-haplotype carrier data frame (same NULL conditions);
mhcExportTables, a list of the summary, de-identified
carriers and manifest data frames captured at "Generate
De-Identified Export Preview" (or NULL before then, without a
pedigree, or while any MHC-file animal is absent from the pedigree);
and mhcExportConfirmed, FALSE until the MHC export's
confirm-gate modal is accepted for the current preview.
Details
A sixth tab, "Linkage and LD Block Metrics" (issue #153 Slice 5), wires in
three additional analyses. A locus-metadata file (locus,
chrom, pos, optionally cM) is validated and
classified into a three-tier coverage report
(checkLocusMetadata, D2). The realized-relatedness-variance
table (markerRealizedRelatednessVariance, D3a) needs only
the existing kinshipMatrix/pedigree plus a curator-supplied
chromosome count and genetic-map length – no genotype file at all. The
LD-block table (markerLdBlock, D3b) reads its OWN,
dedicated linkageGenotypeFile upload – deliberately independent
of the other five tabs' shared genotypeFile, since Shiny renders
every tabPanel's output bindings regardless of which tab is
visible: a multiallelic file uploaded through the shared input would
break the other five tabs' own DT outputs simultaneously, not just this
tab's. Validated through the multiallelic-tolerant sibling validator
(checkLinkageMarkerGenotypeFile) rather than
checkSequenceGenotypeFile, the validator for the shared
upload. Any exported LD-block
table is de-identified (obfuscateLdBlocks) behind a
curator confirm-gate reusing modDeidentifiedExportServer's
tested Generate-Preview -> Confirm -> Confirm-OK pattern (D9).
A seventh tab, "Genomic ROH (F_ROH)" (issue #152 Slice 5), computes
computeGenomicROH from the shared genotype and
locus-metadata uploads, with the same confirm-gated, de-identified
export pattern (genotype matrix, F_ROH table, manifest).
An eighth tab, "MHC Haplotype Reporting" (issue #148 Slice 4), reads its
OWN dedicated mhcHaplotypeFile upload (validated by
checkMhcHaplotypeFile) and reports
mhcHaplotypeFrequency's per-haplotype summary and
mhcHaplotypeCarriers's rare-haplotype carrier list at the
two rarity thresholds shown next to the tables, with a persistent
descriptive-only caveat, the call counts and frequency denominator, and
(when pedigree is available) how many pedigree animals have a
designation. Its export (summary, carrier list aliased through
obfuscateMhcHaplotypes, and a manifest) goes through the
same confirm gate. The alias map covers pedigree animals only, so the
export is not generated – with the reason shown – while any animal in
the MHC file is absent from the loaded pedigree.
This module never touches the existing single-locus genotype path
(checkGenotypeFile/addGenotype/hasGenotype/
getGVGenotype/geneDrop) – the D1 long-format schema is a
new, sibling concern.
See also
Other Shiny modules:
modBreedingGroupsServer(),
modBreedingGroupsUI(),
modCrossCenterIdentityServer(),
modCrossCenterIdentityUI(),
modDeidentifiedExportServer(),
modDeidentifiedExportUI(),
modGeneticDiversityServer(),
modGeneticDiversityUI(),
modGeneticValueServer(),
modGeneticValueUI(),
modGvAndBgDescServer(),
modGvAndBgDescUI(),
modInputServer(),
modInputUI(),
modMarkerGeneticsUI(),
modMatePairServer(),
modMatePairUI(),
modORIPReportingServer(),
modORIPReportingUI(),
modPedigreeServer(),
modPedigreeUI(),
modPotentialParentsServer(),
modPotentialParentsUI(),
modPyramidServer(),
modPyramidUI(),
modSnapshotTrendsServer(),
modSnapshotTrendsUI(),
modSummaryStatsServer(),
modSummaryStatsUI()