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Build a ColocBoostResult

Source: R/ColocBoostResult.R
ColocBoostResult.Rd

Assemble a ColocBoostResult from the raw objects colocboost::colocboost() returns. Callers normally get one from colocboostPipeline rather than building it directly.

Usage

ColocBoostResult(
  results,
  analysis,
  gwasStudy = NA_character_,
  outcomeInfo = NULL,
  ldSketch = NULL,
  computingTime = list(),
  includeUncolocalized = TRUE
)

Arguments

results

A named list of colocboost objects, one per analysis (xqtl_coloc, joint_gwas, or one entry per GWAS study for separate_gwas). NULL entries – a run that failed or was not requested – are skipped.

analysis

Character vector, parallel to results, naming the analysis each element came from.

gwasStudy

Optional character vector, parallel to results, naming the GWAS study for the per-study separate_gwas runs.

outcomeInfo

Data frame mapping outcome name to study, context, trait and dataForm.

ldSketch

Optional genotype panel (see readGenotypes).

computingTime

Optional list of per-analysis timings.

includeUncolocalized

Keep the outcome-specific (uncolocalized) sets as elements flagged isColocalized = FALSE. Default TRUE: dropping them at write time would make "no colocalization here" and "no signal here" indistinguishable downstream.

Value

A ColocBoostResult.

See also

ColocResult, colocboostPipeline

Examples

# Built from `colocboost` objects, which colocboostPipeline() supplies;
# colocboostResultExample is one such result, from a real run.
data(colocboostResultExample)
colocboostResultExample
#> ColocBoostResult with 1 confidence set(s)
#>   colocalized : 1 
#>   outcome-only: 0 
#>   analyses    : xqtl_coloc 
#>   variants    : 1 across all sets
#>   max cos_npc : 0.9938 
# Its unit is a SET of colocalized outcomes rather than a pair, so one row
# can carry any number of them.
colocboostResultExample$outcomes
#> CharacterList of length 1
#> [[1]] eQTL_GENESIM1 psiQTL_GENESIM1
getColocPairs(colocboostResultExample)$nOutcomes
#> [1] 2
# A run that failed or was not requested arrives as NULL and is skipped,
# giving an empty result rather than an error.
nrow(ColocBoostResult(list(NULL), "xqtl_coloc"))
#> [1] 0